Courses & Conferences
Bioconductor provides training in computational and statistical methods for the analysis of genomic data. You are welcome to use material from previous courses. However, you may not include these in separately published works (articles, books, websites). When using all or parts of the Bioconductor course materials (slides, vignettes, scripts) please cite the authors and refer your audience to the Bioconductor website.
Upcoming events are advertised 6 to 8 weeks in advance.
| Keyword | Title | Course | Materials | Date | Bioc/R Version |
|---|---|---|---|---|---|
| Course | CSAMA: Statistical Data Analysis for Genome Scale Biology, Various | CSAMA2022 | html | 2022‑06‑19 | 3.16/4.2 |
| Talk | Visualization and analysis of highly multiplexed imaging data, Nils Eling | SpatialSeminar | slides, video | 2022‑03‑28 | 3.15/4.2 |
| Talk | Analysing Spatially Resolved Transcriptomics Data with Bioconductor, Helena Crowell | SpatialSeminar | slides, video | 2022‑01‑31 | 3.15/4.2 |
| Talk | Spatial Transcriptomics Technologies and Analysis Tools, Dario Righelli | SpatialSeminar | slides, video | 2022‑01‑31 | 3.15/4.2 |
| Talk | The R-universe Build Infrastructure, Jeroen Ooms | BiocDevelForum | slides, video | 2021‑11‑18 | 3.15/4.2 |
| Talk | Translating R package documentation, Martin Morgan | BiocDevelForum | slides, video | 2021‑06‑17 | 3.14/4.1 |
| Talk | HCA / Bioconductor Seed Network Symposium, Various | HCA | video | 2021‑06‑15 | 3.13/4.1 |
| Workshop | Week 7: Participant stories, Various | AnVILpopup | material, video | 2021‑06‑14 | 3.13/4.1 |
| Workshop | Week 6: Reproducible research with AnVILPublish, Martin Morgan | AnVILpopup | material, video | 2021‑06‑07 | 3.13/4.1 |
| Talk | Discussion of changes in R-4.1, Martin Morgan, Mike Smith | BiocDevelForum | video | 2021‑05‑27 | 3.13/4.1 |
| Workshop | Week 5: Using AnVIL for teaching R / Bioconductor, Levi Waldron | AnVILpopup | material, video | 2021‑05‑24 | 3.13/4.1 |
| Workshop | Week 4: Single-cell RNASeq with ‘Orchestrating Single Cell Analysis’ in R / Bioconductor, Vince Carey | AnVILpopup | material, video | 2021‑05‑17 | 3.13/4.1 |
| Workshop | Week 3: Running a Workflow, Martin Morgan, Kayla Interdonato | AnVILpopup | material, video | 2021‑05‑10 | 3.13/4.1 |
| Workshop | Week 2: The R / Bioconductor AnVIL package, Martin Morgan, Nitesh Turaga | AnVILpopup | material, video | 2021‑05‑03 | 3.13/4.1 |
| Workshop | Week 1: Using R / Bioconductor in AnVIL, Martin Morgan | AnVILpopup | material, video | 2021‑04‑26 | 3.13/4.1 |
| Talk | Release schedule discussion, Various | BiocDevelForum | video | 2021‑04‑15 | 3.13/4.1 |
| Talk | Updates to default caching location, Lori Shepherd | BiocDevelForum | slides, video | 2021‑04‑15 | 3.13/4.1 |
| Talk | R7 for Bioconductor, Michael Lawrence | BiocDevelForum | slides, video | 2021‑03‑18 | 3.13/4.1 |
| Talk | Testing R Packages, Dirk Eddelbuettel | BiocDevelForum | slides, video | 2021‑02‑25 | 3.13/4.1 |
| Talk | Bioconductor - Microsoft Genomics, Jass Bagga, Erdal Cosgun | BiocDevelForum | slides, video | 2021‑01‑21 | 3.13/4.1 |
| Talk | Say Hello to ALTREP, Jiefei Wang | BiocDevelForum | slides, video | 2020‑12‑10 | 3.13/4.1 |
| Talk | Alternate Representations of R Objects or ALTREP, Gabe Becker | BiocDevelForum | slides, github, video | 2020‑11‑19 | 3.13/4.1 |
| Talk | Presentation on sparseMatrixStats, Constantin Ahlmann-Eltze | BiocDevelForum | slides, video | 2020‑10‑22 | 3.12/4.0 |
| Talk | Presentation on AnVIL, Martin Morgan | BiocDevelForum | video | 2020‑09‑24 | 3.12/4.0 |
| Talk | Q&A about upcoming release, Lori Shepherd | BiocDevelForum | video | 2020‑09‑24 | 3.12/4.0 |
| Talk | Browsing and searching the Bioconductor codebase, Mike Smith | BiocDevelForum | slides, video | 2020‑08‑20 | 3.12/4.0 |
| Talk | Compiling the OSCA book on the Bioconductor build system, Aaron Lun | BiocDevelForum | video | 2020‑08‑20 | 3.12/4.0 |
| Talk | New builder update, Hervé Pagès | BiocDevelForum | video | 2020‑08‑20 | 3.12/4.0 |
| Conference | Where Software and Biology Connect, Various | BioC2020 | Talks & Workshops | 2020‑07‑27 | 3.12/4.0 |
| Talk | Challenges and opportunities, Kasper Hansen | HCA | slides, video | 2020‑07‑20 | 3.12/4.0 |
| Talk | Data access and representation, Martin Morgan, Daniel van Twisk, Marcel Ramos | HCA | slides, video | 2020‑07‑20 | 3.12/4.0 |
| Talk | Introduction, Martin Morgan | HCA | slides, video | 2020‑07‑20 | 3.12/4.0 |
| Talk | Methods for emerging data, Greg Finak, Matt Ritchie | HCA | slides, video | 2020‑07‑20 | 3.12/4.0 |
| Talk | Methods for scalable, performant analysis, Davide Risso, Aedin Culhane | HCA | slides, video | 2020‑07‑20 | 3.12/4.0 |
| Talk | Outreach, Stephanie Hicks | HCA | slides, video | 2020‑07‑20 | 3.12/4.0 |
| Talk | Continuous integration with Github Actions, Sean Davis | BiocDevelForum | github, video | 2020‑07‑16 | 3.12/4.0 |
| Talk | BiocCheck-a-thon check in, Various | BiocDevelForum | video | 2020‑05‑21 | 3.12/4.0 |
| Talk | Discussion about unit testing, Various | BiocDevelForum | video | 2020‑04‑16 | 3.11/4.0 |
| Talk | Writing our first Bioconductor package as members of the CDSB community, Joselyn Chávez, Carmina Barberena Jonas, Emiliano Sotelo | BiocDevelForum | pdf, video | 2020‑04‑16 | 3.11/4.0 |
| Talk | Bioc vs. CRAN build systems, Various | BiocDevelForum | video | 2020‑03‑19 | 3.11/4.0 |
| Talk | Bioconductor and R 4.0, Lori Shepherd | BiocDevelForum | pdf, video | 2020‑03‑19 | 3.11/4.0 |
| Talk | Quantifying and lightening the package dependency burden, Robert Castelo | BiocDevelForum | pdf, video | 2020‑02‑20 | 3.11/4.0 |
| Talk | Update: Bioconductor Images, Nitesh Turaga | BiocDevelForum | pdf, video | 2020‑02‑20 | 3.11/4.0 |
| Talk | Windows and Rtools 4.0, Mike Smith | BiocDevelForum | pdf, video | 2020‑01‑23 | 3.11/4.0 |
| Workshop | R packages for communicating reproducible research, Martin Morgan | R-IISA | html; Rmd; github | 2019‑12‑26 | 3.10/3.6.1 |
| Talk | Adding additional compression filters to rhdf5, Mike Smith | BiocDevelForum | pdf, video | 2019‑12‑19 | 3.10/3.6 |
| Talk | Update from EuroBioc2019 user/developer sessions, Various authors | BiocDevelForum | pdf, video | 2019‑12‑19 | 3.10/3.6 |
| Talk | Bioconductor updates and directions, Martin Morgan | BiocEurope | slides | 2019‑12‑09 | 3.10/3.6.1 |
| Talk | Bioconductor updates, Martin Morgan | BiocAsia | slides | 2019‑12‑05 | 3.10/3.6.1 |
| Talk | How to advance science using Bioconductor, Martin Morgan | BiocAsia | slides | 2019‑12‑05 | 3.10/3.6.1 |
| Workshop | R and Bioconductor for Genomic Analysis, Martin Morgan | BiocAsia | Rmd; html | 2019‑12‑05 | 3.10/3.6.1 |
| Talk | Bioconductor and R 4.0, Lori Shepherd, Hervé Pagès | BiocDevelForum | pdf, video | 2019‑11‑21 | 3.11/4.0 |
| Talk | Improving findability of BioC packages, Steffen Neumann | BiocDevelForum | pdf, video | 2019‑11‑21 | 3.10/3.6 |
| Workshop | Cancer Immuno-Oncology: Bioconductor and beyond, Martin Morgan | CMCM | Rmd, html | 2019‑11‑18 | 3.10/3.6 |
| Talk | Discussion: Guidelines for submitting data to ExperimentHub, Stephanie Hicks | BiocDevelForum | pdf, video | 2019‑10‑17 | 3.9/3.6 |
| Workflow | Orchestrating Single-Cell Analysis with Bioconductor, Various authors | OSCA | online book | 2019‑10‑10 | 3.9/3.6 |
| Talk | HCA Data Access, Daniel van Twisk | HCA | pptx | 2019‑10‑03 | 3.9/3.6 |
| Talk | Introduction to DataFrames and the impact of recent changes, Hervé Pagès | BiocDevelForum | pdf, video | 2019‑09‑19 | 3.9/3.6 |
| Talk | Pitfalls and best practices for serializing Bioconductor objects, Lori Shepherd | BiocDevelForum | pdf, video | 2019‑09‑19 | 3.9/3.6 |
| Talk | Surprises from scalable container and cloud-based R / Bioconductor deployments, Martin Morgan | DSC | slides | 2019‑09‑18 | 3.9/3.6 |
| Talk | Presentation/discussion on biomaRt, recent issues & future plans, Mike Smith | BiocDevelForum | pdf, video | 2019‑08‑15 | 3.9/3.6 |
| Talk | Single cell updates, Aaron Lun | BiocDevelForum | pptx, video | 2019‑08‑15 | 3.9/3.6 |
| Course | CSAMA: Statistical Analysis for Genome Scale Biology, various authors, Various | CSAMA2019 | html | 2019‑07‑22 | 3.9/3.6 |
| Big data | Evening session: Efficient R, Martin Morgan | CSAMA2019 | html, Rmd | 2019‑07‑22 | 3.9/3.6 |
| introduction | Lab 1: Introduction to R and Bioconductor, Martin Morgan | CSAMA2019 | html | 2019‑07‑22 | 3.9/3.6 |
| Big data | Lab 9-1: Efficient and Parallel Evaluation, Martin Morgan | CSAMA2019 | html, Rmd | 2019‑07‑22 | 3.9/3.6 |
| GSEA | Lecture 19: Gene Set Enrichment Analysis, Martin Morgan | CSAMA2019 | pdf; example html, Rmd | 2019‑07‑22 | 3.9/3.6 |
| introduction | Lecture 1: Introduction to R and Bioconductor, Martin Morgan | CSAMA2019 | html | 2019‑07‑22 | 3.9/3.6 |
| Big data | Lecture 20-1: Working with Large Data, Martin Morgan | CSAMA2019 | html, Rmd | 2019‑07‑22 | 3.9/3.6 |
| Keynote | How Bioconductor advances science and contributes to R, Martin Morgan | useR! 2019 | slides, video | 2019‑07‑12 | 3.9/3.6 |
| Intro | 01: Introduction to R and Bioconductor, Martin Morgan | BSS2019 | html, R, Rmd | 2019‑07‑01 | 3.9/3.6 |
| Intro | 02: Practical: R / Bioconductor and Reproducible Research, Martin Morgan | BSS2019 | html, R, Rmd | 2019‑07‑01 | 3.9/3.6 |
| Intro | 03: Core approaches in Bioconductor, Martin Morgan | BSS2019 | html, R, Rmd | 2019‑07‑01 | 3.9/3.6 |
| Intro | 04: Practical: Organizing data with SummarizedExperiment, Martin Morgan | BSS2019 | html, R, Rmd | 2019‑07‑01 | 3.9/3.6 |
| Intro | 05: Bioconductor Annotation Resources, Martin Morgan | BSS2019 | html, R, Rmd | 2019‑07‑01 | 3.9/3.6 |
| Intro | 06: Gene Set Enrichment – Introduction, Martin Morgan | BSS2019 | pdf, Rnw | 2019‑07‑01 | 3.9/3.6 |
| Intro | 06: Gene Set Enrichment Analysis, Martin Morgan | BSS2019 | html, R, Rmd | 2019‑07‑01 | 3.9/3.6 |
| Conference | Workshops, Various | BioC2019 | workshops | 2019‑06‑26 | 3.9/3.6 |
| Talk | R / Bioconductor for open-source analysis and comprehension of high-throughput genomic data, Martin Morgan | BioME-2019 | slides | 2019‑04‑15 | 3.9/3.6 |
| Workshop | Bioconductor for Everyone: Exploring, Analyzing and Visualizing Large Data Sets in R, Martin Morgan | CDSE-2019 | Rmd, html | 2019‑04‑11 | 3.9/3.6 |
| Workshop | Developing robust and efficient code, Martin Morgan | NURDS | html | 2019‑04‑04 | 3.9/3.6 |
| Talk | Benchmarking on-disk file formats for single-cell data, Raphael Gottardo, Mike Jiang | HCA | slides, video | 2019‑02‑20 | 3.9/3.6 |
| Talk | Developments in rhdf5, Mike Smith | HCA | slides, video | 2019‑02‑20 | 3.9/3.6 |
| Talk | HCABrowser for discovery and access, Daniel van Twisk | HCA | video | 2019‑02‑20 | 3.9/3.6 |
| Talk | HCAMatrixBrowser for retrieving count matrices, Marcel Ramos | HCA | video | 2019‑02‑20 | 3.9/3.6 |
| Talk | New Bioconductor packages for HCA Analysis, Aaron Lun | HCA | slides, video | 2019‑02‑20 | 3.9/3.6 |
| Talk | Ontology issues, Vincent Carey | HCA | slides, shiny, video | 2019‑02‑20 | 3.9/3.6 |
| Talk | Orchestrating single cell analysis with Bioconductor, Stephanie Hicks | HCA | slides, video | 2019‑02‑20 | 3.9/3.6 |
| Talk | State of PCA, Kasper Hansen | HCA | slides, video | 2019‑02‑20 | 3.9/3.6 |
| Talk | Work in Progress: Bioconductor and the HCA, Martin Morgan | HCA | slides, video | 2019‑02‑20 | 3.9/3.6 |
| Talk | mbkmeans for clustering data with lots of samples, Davide Risso | HCA | slides, video | 2019‑02‑20 | 3.9/3.6 |
| Introduction | 100: R and Bioconductor for everyone: an introduction, Martin Morgan, Lori Shepherd | BioC2018 | html | 2018‑07‑25 | 3.8/3.5 |
| Introduction | 101: Introduction to Bioconductor annotation resources, James MacDonald, Lori Shepherd | BioC2018 | html | 2018‑07‑25 | 3.8/3.5 |
| Genomic Ranges | 102: Solving common bioinformatic challenges using GenomicRanges, Michael Lawrence | BioC2018 | html | 2018‑07‑25 | 3.8/3.5 |
| Annotation | 103: Public data resources and Bioconductor, Levi Waldron, Benjamin Haibe-Kains, Sean Davis | BioC2018 | html | 2018‑07‑25 | 3.8/3.5 |
| RNAseq | 200: RNA-seq analysis is easy as 1-2-3 with limma, Glimma, and edgeR, Charity Law | BioC2018 | html | 2018‑07‑25 | 3.8/3.5 |
| RNAseq | 201: RNA-seq data analysis with DESeq2, Michael Love, Simon Anders, Wolfgang Huber | BioC2018 | html | 2018‑07‑25 | 3.8/3.5 |
| Single-cell | 202: Analysis of single-cell RNA-seq data: Dimensionality reduction, clustering, and lineage inference, Diya Das, Kelly Street, Davide Risso | BioC2018 | html | 2018‑07‑25 | 3.8/3.5 |
| Enrichment | 210: Functional enrichment analysis of high-throughput omics data, Ludwig Geistlinger, Levi Waldron | BioC2018 | html | 2018‑07‑25 | 3.8/3.5 |
| Omics | 220: Workflow for multi-omics analysis with MultiAssayExperiment, Marcel Ramos, Ludwing Geistlinger, Levi Waldron | BioC2018 | html | 2018‑07‑25 | 3.8/3.5 |
| Network analysis | 230: Cytoscape automation in R using Rcy3, Ruth Isserlin, Brendan Innes, Jeff Wong, Gary Bader | BioC2018 | html | 2018‑07‑25 | 3.8/3.5 |
| Genomic data | 240: Fluent genomic data analysis with plyranges, Stuart Lee, Michael Lawrence | BioC2018 | html | 2018‑07‑25 | 3.8/3.5 |
| Genomic data | 250: Working with genomic data in R with the DECIPHER package, Nicholas Cooley | BioC2018 | html | 2018‑07‑25 | 3.8/3.5 |
| Biomarker | 260: Biomarker discovery from large pharmacogenomics datasets, Zhaleh Safikhani, Petr Smirnov, Benjamin Haibe-Kains | BioC2018 | html | 2018‑07‑25 | 3.8/3.5 |
| Large data | 500: Effectively using the DelayedArray framework to support the analysis of large datasets, Pete Hickey | BioC2018 | html | 2018‑07‑25 | 3.8/3.5 |
| Packages | 510: Maintaining your Bioconductor package, Nitesh Turaga | BioC2018 | html | 2018‑07‑25 | 3.8/3.5 |
| Conference | BioC 2018: Where Software and Biology Connect, Various authors | BioC2018 | book | 2018‑07‑25 | 3.8/3.5 |
| Talk | Conducting Genomic Symphonies with Bioconductor, Michael Lawrence | BioInfoSummer17 | pdf, zip | 2017‑12‑4 | 3.6/3.4 |
| Conference | Day 1 European Bioconductor Meeting 2017, Various authors | EuroBioc2017 | video | 2017‑12‑5 | 3.6/3.4 |
| Conference | Day 2 European Bioconductor Meeting 2017, Various authors | EuroBioc2017 | video | 2017‑12‑5 | 3.6/3.4 |
| Talk | File Management: BiocFileCache, AnnotationHub, ExperimentHub, Lori Shepherd | EuroBioc2017 | slides | 2017‑12‑5 | 3.6/3.4 |
| Talk | The Bioconductor Project: Current Status, Martin Morgan | EuroBioc2017 | pdf, github | 2017‑12‑5 | 3.6/3.4 |
| Talk | The Bioconductor Project: Current Status, Martin Morgan | BiocAsia2017 | pdf, github | 2017‑11‑17 | 3.6/3.4 |
| Devel | Bioconductor Masterclass: Package Development, Martin Morgan | BiocAsia2017 | html, R, Rmd, github | 2017‑11‑16 | 3.6/3.4 |
| Intro | Bioconductor Masterclass: Bioconductor Essentials, Martin Morgan | BiocAsia2017 | html, R, Rmd, github | 2017‑11‑16 | 3.6/3.4 |
| Intro | R and Bioconductor for Genomic Analysis, Martin Morgan | OSU | Using R html, Rmd; Data Input and Manipulation html, Rmd; Statistics and Graphics html, Rmd; Introduction to Bioconductor html, Rmd; Bioconductor Building Blocks html, Rmd; An RNA-seq Work Flow html, Rmd; Appendix: Quantifying Gene Expression Using salmon html, Rmd | 2017‑09‑11 | 3.6/3.4 |
| Genomic Ranges | A Journey of Discovery through the GenomicRanges Infrastructure, Michael Lawrence | BioC2017 | pdf slides, R, Github | 2017‑07‑26 | 3.6/3.4 |
| Conference | BioC2017: Where Software and Biology Connect, Various authors | BioC2017 | Course material | 2017‑07‑26 | 3.6/3.4 |
| Cloud | Cloud and other creative approaches to working with big data, Vincent Carey, Sean Davis | BioC2017 | Workshop Github | 2017‑07‑26 | 3.6/3.4 |
| RNA | Design and evaluate guide RNAs for CRISPR-Cas9 genome-editing using CRISPRseek and GUIDEseq, Lihua Julie Zhu | BioC2017 | pdf slides, Github CRISPRdemo: html, R, Rmd GUIDEseqdemo: html, R, Rmd |
2017‑07‑26 | 3.6/3.4 |
| Best Practices | Developer best practices, Martin Morgan, Kasper Hansen | BioC2017 | Unit tests, Efficiency, Query Web Resource, Coding Style, Common Bioconductor Classes and Import | 2017‑07‑26 | 3.6/3.4 |
| Workflows | Differential Gene Expression analysis using R and Bioconductor, Radhika Khetani, Meeta Mistry, Mary Piper | BioC2017 | Workflow | 2017‑07‑26 | 3.6/3.4 |
| Enrichment | Ensembl gene set enrichment analysis with EGSEA, Matt Ritchie | BioC2017 | EGSEA workflow: html, R, Rmd Github |
2017‑07‑26 | 3.6/3.4 |
| Enrichment | Functional enrichment analysis of high-throughput omics data in Bioconductor, Ludwig Geistlinger, Levi Waldron | BioC2017 | pdf slides, Github enrichOmics: html, R, Rmd |
2017‑07‑26 | 3.6/3.4 |
| Git | Git with the program: new Bioconductor version control, Nitesh Turaga | BioC2017 | pdf slides | 2017‑07‑26 | 3.6/3.4 |
| ChIP-seq | Integrative analysis and visualization of ChIP-seq data using ChIPpeakAnno , GeneNetworkBuilder, and TrackViewer, Jianhong Ou, Lihua Julia Zhu, Jun Yu | BioC2017 | pdf slides, Github Workflow: html, R, Rmd ChIPseq_stepBystep: html, R, Rmd |
2017‑07‑26 | 3.6/3.4 |
| Introduction | Integrative analysis workshop with TCGAbiolinks and ELMER, Tiago Chedraoui Silva, Houtan Noushmehr, Benjamin Berman | BioC2017 | Analysis: html, R, Rmd AnalysisGui: html, R, Rmd Data: html, R, Rmd DataGui: html, R, Rmd Github, Workshop Link |
2017‑07‑26 | 3.6/3.4 |
| Visualization | Interactive visualization and data analysis with epiviz web components, Jayaram Kancherla, Hector Corrada Bravo, Brian Gottfried | BioC2017 | data preprocessing: html, R, Rmd minfi: html, R, Rmd Bioc2017 Addendum: html, R, Rmd Github |
2017‑07‑26 | 3.6/3.4 |
| Introduction | Introduction to R and Bioconductor, Lori Shepherd | BioC2017 | Intro course: Github | 2017‑07‑26 | 3.6/3.4 |
| Packages | Introduction to new package development and submission, Lori Shepherd | BioC2017 | Make A Package: html, Github | 2017‑07‑26 | 3.6/3.4 |
| RNAseq | Learn to leverage 70,000 human RNA-seq samples for your projects, Leonardo Collado Torres | BioC2017 | pdf slides, Github recount workshop: html, R, Rmd |
2017‑07‑26 | 3.6/3.4 |
| Microbiome | Microbiome Data Analysis, Levi Waldron, Susan Holmes, Pau J. McMurdie, Edoardo Pasolli, Joe Paulson, Lucas Schiffer, Justin Wagner | BioC2017 | MicrobiomeWorkshop: html, R, Rmd MicrobiomeWorkshop II: html, R, Rmd Github |
2017‑07‑26 | 3.6/3.4 |
| Omics | Multi-omics data representation and analysis with MultiAssayExperiment, Marcel Ramos, Levi Waldron | BioC2017 | MAE lab: html, R, Rmd Github |
2017‑07‑26 | 3.6/3.4 |
| Annotation | Understanding Bioconductor Annotation Packages, James MacDonald | BioC2017 | Workshop: html, R, Rmd Github |
2017‑07‑26 | 3.6/3.4 |
| Annotation | Variant Annotation Workshop with FunciVAR, StateHub, and MotifBreakR, Dennis J. Hazelett, Simon G Coetzee | BioC2017 | Workshop Link: html | 2017‑07‑26 | 3.6/3.4 |
| Large Data | Working with large arrays: the DelayedArray package, Hervé Pagès | BioC2017 | Working with large arrays: pdf slides, R, Rnw | 2017‑07‑26 | 3.6/3.4 |
| Single-cell | Bioconductor workflow for single-cell RNA-seq data analysis: dimensionality reduction, clustering, and pseudotime ordering, Fanny Perraudeau, Kelly Street, Davide Risso, Sandrine Dudoit, Elizabeth Purdom | BioC2017 | pdf slides, Github Workshop: html, R, Rmd |
2017‑07‑26 | 3.6/3.4 |
| Workflows | CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets, Malgorzata Nowicka, Lukas M. Weber, Mark D. Robinson | BioC2017 | Workshop: html, Rmd pdf, Github, Workflow |
2017‑07‑26 | 3.6/3.4 |
| Advanced | Advanced R and Bioconductor, Martin Morgan, Hervé Pagès | U. Zurich | Inside the mind of R, R data and algorithms, S4 classes and methods, Doing R better | 2017‑06‑19 | 3.6/3.4 |
| Introduction | CSAMA: Statistical Analysis for Genome Scale Biology, Various authors | CSAMA2017 | Course material | 2017‑06‑11 | 3.5/3.4 |
| Introduction | Introduction to R and Bioconductor, Martin Morgan | OMRF | Install, Intro to R, Data input and manipulation, Statistics, Organization and Graphics, Intro to Bioconductor, Key classes and methods, An RNA-seq work flow, A ChIP-seq workflow | 2017‑05‑08 | 3.5/3.4 |
| Talk | Good software: simple, tidy, rich, Martin Morgan | Meetup | 2017‑04‑20 | 3.5/3.4 | |
| Introduction | Introduction to R and Bioconductor, Martin Morgan, Lori Shepherd | Moffitt | Install, Intro to R, Data input and manipulation, Statistics, Graphics, Intro to Bioconductor, Key classes and methods, An RNA-seq work flow, Next steps | 2017‑03‑02 | 3.4/3.3 |
| Packages | Software development in R and Bioconductor, Martin Morgan | UIdaho | Packages & version control | 2017‑01‑31 | 3.4/3.3 |
| Overview | R / Bioconductor for ‘Omics Analysis (U. Idaho), Martin Morgan | pdf (slides) | 2017‑01‑30 | 3.4/3.3 | |
| Introduction | Introduction to R, Martin Morgan | RPCI RIntro | Installation, Using R, Input and manipulation, Statistics, Workflows and visualization | 2017‑01‑09 | 3.4/3.3 |
| Overview | Bioconductor for ‘Omics Analysis (University of Rochester Medical Center), Martin Morgan | pdf (slides) | 2016‑12‑01 | 3.4/3.3 | |
| RNAseq | An RNA-seq work flow, Martin Morgan | Technion-BKU | html, R, Rmd | 2016‑11‑20 | 3.4/3.3 |
| Annotation | Annotation, Communication, and Performance, Martin Morgan | Technion-BKU | html, R, Rmd | 2016‑11‑20 | 3.4/3.3 |
| Introduction | Introduction to Bioconductor, Martin Morgan | Technion-BKU | html, R, Rmd | 2016‑11‑20 | 3.4/3.3 |
| Status | The Bioconductor Project: Current Status, Martin Morgan | BiocAsia2016 | pdf (slides) | 2016‑11‑04 | 3.4/3.3 |
| Introduction | Bioconductor for Genomic Analysis, Martin Morgan | BiocAsia2016 | html, R, Rmd, github | 2016‑11‑03 | 3.4/3.3 |
| Overview | R / Bioconductor for ‘Omics Analysis (CMRI, Sydney), Martin Morgan | pdf (slides) | 2016‑10‑31 | 3.4/3.3 | |
| Introduction | Reproducible Research in R / Bioconductor (CMRI, Sydney), Martin Morgan | html, R, Rmd, github | 2016‑10‑31 | 3.4/3.3 | |
| Annotation | Annotating genes, genomes, and variants, Martin Morgan | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Performance | Benchmarking out-of-memory strategies, Vincent J. Carey | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| ChIP-seq | ChIP-Seq analysis basics, Alejandro Reyes; Mike Smith | CSAMA2016 | Rmd html Rpackage | 2016‑07‑10 | 3.4/3.3 |
| Statistics | Clustering, classification, and regression with genomic examples, Vincent J. Carey | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Genomic Ranges | Computing with sequences and ranges, Martin Morgan | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| RNAseq | End-to-end RNA-Seq workflow, Simon Anders; Michael Love; Charlotte Soneson | CSAMA2016 | Rmd html pdf | 2016‑07‑10 | 3.4/3.3 |
| Experimental design | Experimental design, Charlotte Soneson | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Gene set enrichment | Gene set enrichment - Introduction, Martin Morgan | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Gene set enrichment | Gene-sets and correlation, Michael Love | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Graphics | Graphics, Wolfgang Huber | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Sequencing | High-throughput sequencing and using short-read aligners, Simon Anders | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Statistics | Hypothesis testing, Wolfgang Huber | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Statistics | Independent Hypothesis Weighting, Wolfgang Huber | CSAMA2016 | Rmd html | 2016‑07‑10 | 3.4/3.3 |
| Introduction | Introduction to R and Bioconductor, Martin Morgan | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Introduction | Introduction to R and Bioconductor, Martin Morgan | CSAMA2016 | html data Rmd | 2016‑07‑10 | 3.4/3.3 |
| Statistics | Introduction to linear models, Levi Waldron | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Introduction | Learn to love the data frame, Jenny Bryan | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Performance | Machine Learning, Parallelization and performance, Martin Morgan; Vincent J. Carey | CSAMA2016 | Efficient and parallel code html Machine Learning html Rmd pdf Code |
2016‑07‑10 | 3.4/3.3 |
| Statistics | Meta-analysis, Levi Waldron | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Microbiome | Microbial genomics, Charlotte Soneson | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Statistics | Multiple testing, Wolfgang Huber | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| RNAseq | New RNA-seq workflows, Charlotte Soneson | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Performance | Performance and parallel evaluation, Martin Morgan | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| RNAseq | RNA-seq data analysis and differential expression, Michael Love | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Git | Reproducible research and R authoring with markdown and knitr, Jenny Bryan | CSAMA2016 | github | 2016‑07‑10 | 3.4/3.3 |
| Statistics | Resampling methods, Levi Waldron | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Statistics | Robust statistics, Michael Love | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Git | Use of Git and GitHub with R, RStudio, and R Markdown, Jenny Bryan | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Intermediate | What should you do next?, Jenny Bryan | CSAMA2016 | 2016‑07‑10 | 3.4/3.3 | |
| Graphics | R Graphics, Wolfgang Huber | CSAMA2016 | Rmd pdf | 2016‑07‑10 | 3.4/3.3 |
| Methylation | Analysing DNA methylation data with Bioconductor, Peter Hickey, Kasper Hansen | BioC2016 | HTML R Rmd github | 2016‑06‑25 | 3.4/3.3 |
| RNASeq | Analysis of single-cell RNA-seq data with R and Bioconductor, Davide Risso, Kelly Street, Michael Cole | BioC2016 | Cluster: html R Rmd Scone: html R Rmd Slingshot: html R Rmd github |
2016‑06‑25 | 3.4/3.3 |
| RNASeq | Analyzing splice events from RNA-seq data with SGSeq, Leonard Goldstein | BioC2016 | HTML R Rmd github package |
2016‑06‑25 | 3.4/3.3 |
| Annotation | Annotating high throughput data using Bioconductor resources, James MacDonald | BioC2016 | HTML R Rmd github | 2016‑06‑25 | 3.4/3.3 |
| workflows | Building and running automated NGS analysis workflows, Thomas Girke | BioC2016 | SystemPipeR Intro: html R Rmd SystemPipeRdata: html R Rmd github |
2016‑06‑25 | 3.4/3.3 |
| Introduction | Getting to know R and Bioconductor, Valerie Obenchain, Lori Shepherd | BioC2016 | Lecture Overview: html R Rmd github |
2016‑06‑25 | 3.4/3.3 |
| Genomic Ranges | Hello Ranges: An Introduction to Analyzing Genomic Ranges in R, Michael Lawrence | BioC2016 | PDF R Rmd github | 2016‑06‑25 | 3.4/3.3 |
| Visualization | Interactive visualization with epiviz, Héctor Corrada Bravo, Jayaram kancherla, Justin Wagner | BioC2016 | Preprocessing: html R Rmd Minifi: html R Rmd github |
2016‑06‑25 | 3.4/3.3 |
| Statistics | Introduction to Bayesian Inference using Stan with Applications to Cancer Genomics, Jacqueline Buros | BioC2016 | Applied Survival Models: html R Rmd Survival Model Example: html R Rmd github |
2016‑06‑25 | 3.4/3.3 |
| Introduction | Introduction to ImmuneSpaceR, Renan Sauteraud, Lev Dashevskiy, Greg Finak, Raphael Gottardo | BioC2016 | Content: html R Rmd Example: html R Rmd github |
2016‑06‑25 | 3.4/3.3 |
| RNASeq | Low-level exploratory data analysis and methods development for RNA-seq, Michael Love | BioC2016 | HTML R Rmd github | 2016‑06‑25 | 3.4/3.3 |
| Introductoin | Making your packages accessible to non-programmer collaborators using the VisRseq platform, Hamid Younesy, Torsten Möller, Mohammad M. Karimi | BioC2016 | Slides PDF R Rmd Software github |
2016‑06‑25 | 3.4/3.3 |
| Sequence Analysis | Managing big biological sequence data with Biostrings and DECIPHER, Erik Wright | BioC2016 | Slides html R Rmd github | 2016‑06‑25 | 3.4/3.3 |
| Gene set enrichment | Single Cell Differential Expression and Gene Set Enrichment with MAST, Andrew McDavid, Raphael Gottardo, Greg Finak | BioC2016 | Slides PDF R Rmd MAIT Analysis github |
2016‑06‑25 | 3.4/3.3 |
| Omics | The MultiAssayExperiment class for analysis of multi-omics experiments, Levi Waldron, Marcel Ramos, Vince Carey, Kasper Hansen, Martin Morgan | BioC2016 | HTML R Rmd github | 2016‑06‑25 | 3.4/3.3 |
| Cloud | Wrapping Your R tools to Analyze National-Scale Cancer Genomics in the Cloud, Tengfei Yin, Nan Xiao | BioC2016 | api: html R Rmd apps: html R Rmd workflow: html R Rmd cgc-sparql: html R Rmd docker: html R Rmd rstudio: html R Rmd github |
2016‑06‑25 | 3.4/3.3 |
| Intermediate | Writing efficient, scalable code, Martin Morgan | BioC2016 | HTML R Rmd github | 2016‑06‑25 | 3.4/3.3 |
| Proteomics | R / Bioconductor tools for mass spectrometry-based proteomics, Laurent Gatto | BioC2016 | HTML R Rmd github | 2016‑06‑25 | 3.4/3.3 |
| Introduction | China R Conference: Bioconductor for high-throughput genetic data, Martin Morgan | China-R | 2016‑05‑29 | 3.3/3.3 | |
| Introduction | A1: R Intro, Martin Morgan, Lori Shepherd | BiocIntroRPCI | HTML R Rmd | 2016‑05‑16 | 3.3/3.3 |
| Introduction | A2: Input and Manipulation, Martin Morgan, Lori Shepherd | BiocIntroRPCI | HTML R Rmd | 2016‑05‑16 | 3.3/3.3 |
| Introduction | A3: Statistical Analysis, Martin Morgan, Lori Shepherd | BiocIntroRPCI | HTML R Rmd | 2016‑05‑16 | 3.3/3.3 |
| Introduction | A4: Visualization, Martin Morgan, Lori Shepherd | BiocIntroRPCI | HTML R Rmd | 2016‑05‑16 | 3.3/3.3 |
| Introduction | B1: Bioconductor Intro, Martin Morgan, Lori Shepherd | BiocIntroRPCI | HTML R Rmd | 2016‑05‑16 | 3.3/3.3 |
| Introduction | B2: Common Operations, Martin Morgan, Lori Shepherd | BiocIntroRPCI | HTML R Rmd | 2016‑05‑16 | 3.3/3.3 |
| Introduction | B3: RNASeq Workflow, Martin Morgan, Lori Shepherd | BiocIntroRPCI | HTML R Rmd | 2016‑05‑16 | 3.3/3.3 |
| Introduction | B4: Next Steps, Martin Morgan, Lori Shepherd | BiocIntroRPCI | HTML R Rmd | 2016‑05‑16 | 3.3/3.3 |
| Introduction | Introduction to High Throughput DNA Sequence Data Analysis Using R / Bioconductor, Martin Morgan | ENAR 2016 | Rmd R; github | 2016‑04‑08 | 3.2/3.2 |
| Intro | Introduction to Sequence Analysis, R, and Bioconductor: content, Martin Morgan | EMBO 2015 | html, Rmd, R | 2015‑10‑19 | 3.2/3.2 |
| Intro | Introduction to Sequence Analysis, R, and Bioconductor: exercises, Martin Morgan | EMBO 2015 | html, Rmd R | 2015‑10‑19 | 3.2/3.2 |
| Intro | Introduction to Sequence Analysis, R, and Bioconductor: notes, Martin Morgan | EMBO 2015 | html, Rmd, R; github | 2015‑10‑19 | 3.2/3.2 |
| Annotation | Adding Annotation To Your Analysis, Martin Morgan | Uruguay2015 | HTML Rmd R | 2015‑10‑05 | 3.2/3.2 |
| ChIPSeq | ChIP-Seq for Understanding Gene Regulation, Martin Morgan | Uruguay2015 | HTML Rmd R | 2015‑10‑05 | 3.2/3.2 |
| Large Data | Counting Reads And Working With Large Files, Martin Morgan | Uruguay2015 | HTML Rmd R | 2015‑10‑05 | 3.2/3.2 |
| Introduction | Data manipulation, Houtan Noushmehr | Uruguay2015 | HTML Rmd R | 2015‑10‑05 | 3.2/3.2 |
| Microarrays | Gene Expression, Houtan Noushmehr | Uruguay2015 | HTML Rmd R | 2015‑10‑05 | 3.2/3.2 |
| Genomic Ranges | Genomic Ranges For Genome-Scale Data And Annotation, Martin Morgan | Uruguay2015 | HTML Rmd R | 2015‑10‑05 | 3.2/3.2 |
| Introduction | Introduction, Martin Morgan | Uruguay2015 | HTML Rmd R | 2015‑10‑05 | 3.2/3.2 |
| RNASeq | RNA-Seq Differential Expression, Martin Morgan | Uruguay2015 | HTML Rmd R | 2015‑10‑05 | 3.2/3.2 |
| RNASeq | Supplement 1: RNA-Seq Workflow, Martin Morgan | Uruguay2015 | HTML Rmd R | 2015‑10‑05 | 3.2/3.2 |
| RNASeq | Supplement 2: RNA-Seq Statistical Issues, Martin Morgan | Uruguay2015 | HTML Rmd R | 2015‑10‑05 | 3.2/3.2 |
| Data Integration | The TCGAbiolinks package, Houtan Noushmehr | Uruguay2015 | 2015‑10‑05 | 3.2/3.2 | |
| SummarizedExperiment | Working with Data: SummarizedExperiment, Martin Morgan | Uruguay2015 | HTML Rmd R | 2015‑10‑05 | 3.2/3.2 |
| Introduction | Introduction: Analysis and Comprehension, Martin Morgan | BiocAsia2015 | AMI, HTML, Rmd, R | 2015‑09‑07 | 3.2/3.2 |
| Annotation | Workshop: Gene, Genome, and Variant Annotation, Martin Morgan | BiocAsia2015 | AMI, HTML, Rmd, R | 2015‑09‑07 | 3.2/3.2 |
| RNASeq | Workshop: RNASeq, Martin Morgan | BiocAsia2015 | AMI, HTML, Rmd, R | 2015‑09‑07 | 3.2/3.2 |
| Data Representation | Workshop: Sequences, Alignments, and Large Data, Martin Morgan | BiocAsia2015 | AMI, HTML, Rmd, R | 2015‑09‑07 | 3.2/3.2 |
| RNASeq | SGSeq and alternative splicing, Leonard Goldstein | BioC2015 | AMI, HTML, Rmd, R, GitHub | 2015‑07‑20 | 3.2/3.2 |
| RNASeq | Advanced Lab: Explore the Data, Sonali Arora | BioC2015 | AMI, GitHub, HTML, Rmd, R | 2015‑07‑20 | 3.2/3.2 |
| RNASeq | Advanced RnaSeq, Sonali Arora | BioC2015 | AMI, GitHub, HTML, Rmd, R | 2015‑07‑20 | 3.2/3.2 |
| Reproducibility | An introduction to Docker and the Bioconductor Docker containers, Dan Tenenbaum | BioC2015 | AMI, HTML, Rmd, R, GitHub | 2015‑07‑20 | 3.2/3.2 |
| Flow Cytometry | Analysis of Designed Experiments Using OpenCyto, Greg Finak | BioC2015 | AMI, GitHub, HTML, Rmd, R | 2015‑07‑20 | 3.2/3.2 |
| Annotation | Annotation Resources for Bioconductor, Marc Carlson, Sonali Arora | BioC2015 | AMI, GitHub, HTML, Rmd, R | 2015‑07‑20 | 3.2/3.2 |
| Annotation | AnnotationHub Recipes, Marc Carlson, Sonali Arora | BioC2015 | AMI, GitHub, HTML, Rmd, R | 2015‑07‑20 | 3.2/3.2 |
| Workflows | Automated NGS workflows with systemPipeR running on clusters or single machines, with a focus on VAR-seq: systemPipeR, Thomas Girke | BioC2015 | AMI, GitHub, HTML, Rmd, R | 2015‑07‑20 | 3.2/3.2 |
| Image Analysis | Basics of image data and spatial patterns analysis in R, Andrzej Oleś, Wolfgang Huber | BioC2015 | AMI, HTML, Rmd, R, GitHub | 2015‑07‑20 | 3.2/3.2 |
| ChIPSeq | Detecting differential binding in ChIP-seq data with csaw, Aaron Lun | BioC2015 | AMI, HTML, Rmd, R, GitHub | 2015‑07‑20 | 3.2/3.2 |
| RNASeq | Differential expression, manipulation, and visualization of RNA-seq reads, Mike Love | BioC2015 | AMI, HTML, Rmd, R, GitHub | 2015‑07‑20 | 3.2/3.2 |
| Best Practices | FAQ Live! Common questions and expert solutions, delivered in person, James MacDonald | BioC2015 | AMI, PDF, Rnw, R, GitHub | 2015‑07‑20 | 3.2/3.2 |
| Scalable Computing | GoogleGenomics, Nicole Deflaux, Siddhartha Bagaria and Craig Citro | BioC2015 | AMI, GitHub, readthedocs | 2015‑07‑20 | 3.2/3.2 |
| Introduction | Introduction to R, Sonali Arora | BioC2015 | AMI, GitHub, HTML, Rmd, R | 2015‑07‑20 | 3.2/3.2 |
| Introduction | Introduction to Bioconductor, Sonali Arora | BioC2015 | AMI, GitHub, HTML, Rmd, R | 2015‑07‑20 | 3.2/3.2 |
| Introduction | Lab: Basic Bioconductor, Sonali Arora | BioC2015 | AMI, GitHub, HTML, Rmd, R | 2015‑07‑20 | 3.2/3.2 |
| Intermediate | Lab: Intermediate Bioconductor, Sonali Arora | BioC2015 | AMI, GitHub, HTML, Rmd, R | 2015‑07‑20 | 3.2/3.2 |
| Workflows | Liftr & sbgr, Nan Xiao | BioC2015 | AMI, PDF, Video | 2015‑07‑20 | 3.2/3.2 |
| Large Data | Management and analysis of large genomic data., Valerie Obenchain, Martin Morgan | BioC2015 | AMI, HTML, Rmd, R, GitHub | 2015‑07‑20 | 3.2/3.2 |
| Methylation | Methylation and the analysis of Illumina 450k microarrays, Kasper Hansen | BioC2015 | AMI, HTML, Rmd, R, GitHub | 2015‑07‑20 | 3.2/3.2 |
| Genomic Ranges | Practical introduction to Bioconductor foundational data structures for high throughput sequencing analysis, Hervé Pagès, Michael Lawrence | BioC2015 | AMI, PDF, R | 2015‑07‑20 | 3.2/3.2 |
| Omics | TCGAloading, Levi Waldron, Tim Triche, Aedin Culhane | BioC2015 | AMI, GitHub, HTML, Rmd, R | 2015‑07‑20 | 3.2/3.2 |
| Flow Cytometry | Visualize cytometry data with ggcyto, Greg Finak | BioC2015 | AMI, HTML, Rmd, R | 2015‑07‑20 | 3.2/3.2 |
| Omics | multiAssayQC, Levi Waldron, Tim Triche, Aedin Culhane | BioC2015 | AMI, GitHub, HTML, Rmd, R | 2015‑07‑20 | 3.2/3.2 |
| Introduction | Bioconductor for high-throughput sequence analysis, Martin Morgan, Sonali Arora | useR! 2015 | talk, lab; github | 2015‑06‑30 | 3.1/3.2 |
| ChIPSeq | Lab: ChIP-seq analysis basics, Aleksandra Pȩkowska, Simon Anders | CSAMA 2015 | pdf; github | 2015‑06‑15 | 3.1/3.2 |
| RNASeq | Lab: End-to-end RNA-Seq workflow, Mike Love, Simon Anders, Wolfgang Huber | CSAMA 2015 | html; github | 2015‑06‑15 | 3.1/3.2 |
| Visualization | Lab: Interactive data visualization with Shiny, Andrzej Oleś | CSAMA 2015 | html; github | 2015‑06‑15 | 3.1/3.2 |
| Introduction | Lab: Introduction to R and Bioconductor, Martin Morgan | CSAMA 2015 | html; github | 2015‑06‑15 | 3.1/3.2 |
| MachineLearning | Lab: Machine Learning and Parallel Computing, Wolfgang Huber, Martin Morgan | CSAMA 2015 | html; github | 2015‑06‑15 | 3.1/3.2 |
| LargeData | Lab: Performance and Parallel Evaluation, Martin Morgan | CSAMA 2015 | html; github | 2015‑06‑15 | 3.1/3.2 |
| Metagenomics | Lab: Phyloseq Basic Usage for Metagenomics, Paul Pyl | CSAMA 2015 | html; github | 2015‑06‑15 | 3.1/3.2 |
| Variants | Lab: Plotting Regions from BAM files directly, Paul Pyl | CSAMA 2015 | html; github | 2015‑06‑15 | 3.1/3.2 |
| ReproducibleResearch | Lab: Reproducible Research and R Authoring with markdown and knitr, Laurent Gatto | CSAMA 2015 | html; github | 2015‑06‑15 | 3.1/3.2 |
| Technology | Lecture: Basics of sequence alignment and aligners, Simon Anders | CSAMA 2015 | 2015‑06‑15 | 3.1/3.2 | |
| Statistics | Lecture: Clustering and classification, Vincent Carey | CSAMA 2015 | html | 2015‑06‑15 | 3.1/3.2 |
| GenomicRanges | Lecture: Computing with sequences and genomic intervals, Martin Morgan | CSAMA 2015 | pdf, html | 2015‑06‑15 | 3.1/3.2 |
| ChIPSeq | Lecture: Epigenetics and ChIP-Seq, Aleksandra Pȩkowska | CSAMA 2015 | 2015‑06‑15 | 3.1/3.2 | |
| GeneSetEnrichment | Lecture: Gene set enrichment analysis, part I, Martin Morgan | CSAMA 2015 | 2015‑06‑15 | 3.1/3.2 | |
| GeneSetEnrichment | Lecture: Gene set enrichment analysis, part II, Michael Love | CSAMA 2015 | html | 2015‑06‑15 | 3.1/3.2 |
| HiC | Lecture: HiC data analysis, Aleksandra Pȩkowska | CSAMA 2015 | 2015‑06‑15 | 3.1/3.2 | |
| Statistics | Lecture: Hypothesis testing and multiple testing, Wolfgang Huber | CSAMA 2015 | 2015‑06‑15 | 3.1/3.2 | |
| Proteomics | Lecture: Introduction to MS based proteomics and Bioconductor infrastructure, Laurent Gatto | CSAMA 2015 | 2015‑06‑15 | 3.1/3.2 | |
| Introduction | Lecture: Introduction to R and Bioconductor, Martin Morgan | CSAMA 2015 | 2015‑06‑15 | 3.1/3.2 | |
| LargeData | Lecture: Large data, performance, and parallelization; large-scale efficient computation with genomic intervals, Martin Morgan | CSAMA 2015 | 2015‑06‑15 | 3.1/3.2 | |
| RNASeq | Lecture: RNA-Seq data analysis and differential expression part I, Simon Anders | CSAMA 2015 | 2015‑06‑15 | 3.1/3.2 | |
| RNASeq | Lecture: RNA-Seq data analysis and differential expression part II, Michael Love | CSAMA 2015 | 2015‑06‑15 | 3.1/3.2 | |
| RNASeq | Lecture: Single-cell RNA-Seq, Alejandro Reyes, Simon Anders | CSAMA 2015 | 2015‑06‑15 | 3.1/3.2 | |
| Visualization | Lecture: Visualization, the grammar of graphics and ggplot2, Wolfgang Huber | CSAMA 2015 | 2015‑06‑15 | 3.1/3.2 | |
| Annotation | Lecture: Working with annotation - genes, genomic features and variants, Martin Morgan | CSAMA 2015 | pdf, html | 2015‑06‑15 | 3.1/3.2 |
| MOOC | Introduction to Bioconductor, Rafael Irizarry, Michael Love, Vincent Carey | EdX-PH525.4x | html | 2015‑03‑30 | 3.1/3.2 |
| MOOC | Statistics and R for the Life Sciences, Rafael Irizarry, Michael Love | EdX-PH525.1x | html | 2015‑01‑19 | 3.1/3.2 |
| ChIPSeq | ChIP-seq with csaw, Martin Morgan | SeattleApr2015 | html, R, Rmd | 2015‑04‑06 | 3.1/3.2 |
| RNASeq | Differential Gene Expression, Martin Morgan | SeattleApr2015 | html, R, Rmd | 2015‑04‑06 | 3.1/3.2 |
| Gene set enrichment | Gene set enrichment, Martin Morgan | SeattleApr2015 | html, R, Rmd | 2015‑04‑06 | 3.1/3.2 |
| Genomic Ranges | Genomic Ranges, Martin Morgan | SeattleApr2015 | html, R, Rmd | 2015‑04‑06 | 3.1/3.2 |
| Large Data | Integrative Data Analysis, Martin Morgan | SeattleApr2015 | html, R, Rmd | 2015‑04‑06 | 3.1/3.2 |
| Large Data | Large Data, Martin Morgan | SeattleApr2015 | htm, R, Rmd | 2015‑04‑06 | 3.1/3.2 |
| Machine Learning | Machine Learning, Sonali Arora | SeattleApr2015 | html, R, Rmd | 2015‑04‑06 | 3.1/3.2 |
| Methylation | Methylation and regulatory work flows with minfi, Martin Morgan | SeattleApr2015 | html, R, Rmd | 2015‑04‑06 | 3.1/3.2 |
| Intermediate | Use R / Bioconductor for Sequence Analysis, Martin Morgan, Sonali Arora | SeattleApr2015 | package, AMI | 2015‑04‑06 | 3.1/3.2 |
| Genomic Ranges | Genomic Ranges, Martin Morgan, Hervé Pagès | Use Bioc | html, R, Rmd, slides | 2015‑02‑04 | 3.1/3.2 |
| Visualization | Interactive visualization, Martin Morgan, Hervé Pagès | Use Bioc | html, R, Rmd | 2015‑02‑04 | 3.1/3.2 |
| Introduction | Introduction to R / Bioconductor, Martin Morgan, Hervé Pagès | Use Bioc | html, R, Rmd | 2015‑02‑04 | 3.1/3.2 |
| Status Update | New packages and functionality, Martin Morgan, Hervé Pagès | Use Bioc | html, R, Rmd | 2015‑02‑04 | 3.1/3.2 |
| Annotation | Package, web, and hub annotation resources, Martin Morgan, Hervé Pagès | Use Bioc | html, R, Rmd | 2015‑02‑04 | 3.1/3.2 |
| Intermediate | Use R / Bioconductor for Sequence Analysis, Martin Morgan, Hervé Pagès | Use Bioc | package, AMI | 2015‑02‑04 | 3.1/3.2 |
| Large Data | Working with large data, Martin Morgan, Hervé Pagès | Use Bioc | html, R, Rmd | 2015‑02‑04 | 3.1/3.2 |
| Packages | From code to packages, Martin Morgan, Hervé Pagès | Learn Bioc | html, R, Rmd | 2015‑02‑02 | 3.1/3.2 |
| Bioconductor | Introduction to Bioconductor, Martin Morgan, Hervé Pagès | Learn Bioc | html, R, Rmd | 2015‑02‑02 | 3.1/3.2 |
| Sequence Analysis | Introduction to Bioconductor for Sequence Analysis, Martin Morgan, Hervé Pagès | Learn Bioc | html, R, Rmd | 2015‑02‑02 | 3.1/3.2 |
| R | Introduction to R, Martin Morgan, Hervé Pagès | Learn Bioc | html, R, Rmd | 2015‑02‑02 | 3.1/3.2 |
| Reproducibility | Introduction to reproducible analysis, Martin Morgan, Hervé Pagès | Learn Bioc | html, R, Rmd | 2015‑02‑02 | 3.1/3.2 |
| Introduction | Learning R / Bioconductor for Sequence Analysis, Martin Morgan, Hervé Pagès | Learn Bioc | package, AMI | 2015‑02‑02 | 3.1/3.2 |
| Sequence Analysis | Overview of common sequencing work flows, Martin Morgan, Hervé Pagès | Learn Bioc | html, R, Rmd | 2015‑02‑02 | 3.1/3.2 |
| RNASeq | RNA-seq overview and work flow, Martin Morgan, Hervé Pagès | Learn Bioc | slides, lab, R, Rmd | 2015‑02‑02 | 3.1/3.2 |
| Visualization | Visualizing genomic data, Martin Morgan, Hervé Pagès | Learn Bioc | html, R, Rmd | 2015‑02‑02 | 3.1/3.2 |
| Large Data | Working with large data, Martin Morgan, Hervé Pagès | Learn Bioc | html, R, Rmd | 2015‑02‑02 | 3.1/3.2 |
| Introduction | R/Bioconductor for Integrative Genomic Analysis, Martin Morgan | useR! Lyon | slides | 2015‑01‑15 | 3.0/3.1.2 |
| Status Update | Bioconductor Project Update, January 2015, Martin Morgan | BiocEurope2015 | slides | 2015‑01‑12 | 3.1/3.2 |
| Best Practices | Google Hangout for New Package Submitters, Marc Carlson | NewPackages | slides, Video | 2014‑12‑10 | 3.1/3.2 |
| Annotation | Annotating Genes, Genomes, and Variants, Martin Morgan | SeattleOct2014 | html, R, Rmd | 2014‑10‑27 | 3.0/3.1.1 |
| Appendix | Appendix: Install IGV, Martin Morgan | SeattleOct2014 | html, R, Rmd hg19_alias.tab | 2014‑10‑27 | 3.0/3.1.1 |
| Workflows | Common Sequence Analysis Work Flows, Martin Morgan | SeattleOct2014 | html, R, Rmd | 2014‑10‑27 | 3.0/3.1.1 |
| Copy Number | Copy Number, Sonali Arora | SeattleOct2014 | html, R, Rmd | 2014‑10‑27 | 3.0/3.1.1 |
| Gene set enrichment | Gene set enrichment, Martin Morgan | SeattleOct2014 | html, R, Rmd | 2014‑10‑27 | 3.0/3.1.1 |
| Introduction | Introduction, Martin Morgan | SeattleOct2014 | html, R, Rmd | 2014‑10‑27 | 3.0/3.1.1 |
| Bioconductor | Introduction to Bioconductor, Martin Morgan | SeattleOct2014 | html, R, Rmd | 2014‑10‑27 | 3.0/3.1.1 |
| R | Introduction to R, Martin Morgan | SeattleOct2014 | html, R, Rmd | 2014‑10‑27 | 3.0/3.1.1 |
| Machine Learning | Machine Learning, Sonali Arora | SeattleOct2014 | html, R, Rmd | 2014‑10‑27 | 3.0/3.1.1 |
| Packages | Organizing Code in Functions, Files, and Packages, Martin Morgan | SeattleOct2014 | html, R, Rmd | 2014‑10‑27 | 3.0/3.1.1 |
| RNASeq | RNA-Seq, Martin Morgan | SeattleOct2014 | html, R, Rmd | 2014‑10‑27 | 3.0/3.1.1 |
| RNASeq | RNA-Seq Lab: Workflow – gene-level exploratory analysis and differential expression, Michael Love et al. | SeattleOct2014 | html | 2014‑10‑27 | 3.0/3.1.1 |
| Reproducibility | Reproducible Research, Martin Morgan | SeattleOct2014 | html, R, Rmd | 2014‑10‑27 | 3.0/3.1.1 |
| Visualization | Visualization, Martin Morgan | SeattleOct2014 | html, R, Rmd | 2014‑10‑27 | 3.0/3.1.1 |
| Large Data | Working with Large Data, Martin Morgan | SeattleOct2014 | html, R, Rmd | 2014‑10‑27 | 3.0/3.1.1 |
| Methylation | A short methylation analysis using minfi, Martin Morgan | Epigenomics | html R Rmd | 2014‑08‑24 | 2.14/3.1.1 |
| RNASeq | Counting reads for RNA-seq in Bioconductor, Martin Morgan | Epigenomics | pdf R Rnw | 2014‑08‑24 | 2.14/3.1.1 |
| Epigenomics | Introduction to Bioconductor for Epigneomics, Martin Morgan | Epigenomics | pdf R Rnw | 2014‑08‑24 | 2.14/3.1.1 |
| Sequence Analysis | Introduction to Bioconductor for Sequence Analysis, Martin Morgan | Epigenomics | html R Rmd | 2014‑08‑24 | 2.14/3.1.1 |
| R | Introduction to R (slides), Martin Morgan | Epigenomics | html | 2014‑08‑24 | 2.14/3.1.1 |
| RNASeq | Introduction to RNA-Seq data analysis, Benilton Carvalho | Epigenomics | 2014‑08‑24 | 2.14/3.1.1 | |
| Methylation | Introduction to working with methylation arrays (slides), Martin Morgan | Epigenomics | html | 2014‑08‑24 | 2.14/3.1.1 |
| Data Representation | Sequence data represenations in Bioconductor, Martin Morgan | Epigenomics | html R Rmd | 2014‑08‑24 | 2.14/3.1.1 |
| eQTL | eQTL analysis – an approach with Bioconductor, Vincent Carey | Epigenomics | 2014‑08‑24 | 2.14/3.1.1 | |
| Methylation | Analysis of 450k methylation data with the minfi package, Kasper Hansen | BioC2014 | pdf, Rnw, R | 2014‑07‑30 | 2.14/3.1.1 |
| RNASeq | Analysis of RNA-Seq using the DESeq2 package, Michael Love | BioC2014 | pdf, Rnw, R | 2014‑07‑30 | 2.14/3.1.1 |
| Annotation | Bioconductor annotations: using and sharing resources, Marc Carlson | BioC2014 | workflow, vignette | 2014‑07‑30 | 2.14/3.1.1 |
| RNASeq | CRISPRseek: Design of target-specific guide RNAs in CRISPR-Cas9 genome-editing systems, Julie Zhu | BioC2014 | pdf, html, Rmd, R | 2014‑07‑30 | 2.14/3.1.1 |
| RNASeq | Differential gene- and exon-level expression analyses for RNA-seq data using edgeR, voom and featureCounts, Mark Robinson | BioC2014 | pdf, html, md | 2014‑07‑30 | 2.14/3.1.1 |
| eQTL | Genetics of gene expression: computation and integrative prediction, Vincent Carey | BioC2014 | html, Rmd, R | 2014‑07‑30 | 2.14/3.1.1 |
| Pathway | Integrated pathway analysis of multiple omics datasets, Aedin Culhane | BioC2014 | html, Rmd, R | 2014‑07‑30 | 2.14/3.1.1 |
| Genomic Ranges | Learn how to use Bioconductor to perform common tasks on your high-throughput sequencing data, Hervé Pagès | BioC2014 | 2014‑07‑30 | 2.14/3.1.1 | |
| Meta-analysis | Meta-analysis of genomics experiments using Bioconductor, Levi Waldron | BioC2014 | Rpres, R | 2014‑07‑30 | 2.14/3.1.1 |
| Scalable Computing | Parallel Computing with Bioconductor in the Amazon Cloud, Valerie Obenchain | BioC2014 | pdf, R | 2014‑07‑30 | 2.14/3.1.1 |
| R/Bioconductor | R / Bioconductor for everyone, Martin Morgan | BioC2014 | slides, pdf, R | 2014‑07‑30 | 2.14/3.1.1 |
| Proteomics | R / Bioconductor packages for Proteomics, Laurent Gatto | BioC2014 | html, Rmd, R | 2014‑07‑30 | 2.14/3.1.1 |
| Flow Cytometry | Tutorial, Introduction to Flow Cytometry Data Analysis using OpenCyto and Bioconductor, Greg Finak | BioC2014 | html, Rmd, R | 2014‑07‑30 | 2.14/3.1.1 |
| Variants | Variant calling with Bioconductor, Michael Lawrence | BioC2014 | pdf, R, pkg | 2014‑07‑30 | 2.14/3.1.1 |
| ChIPSeq | Visualisation and assessment of ChIP-seq quality using ChIPQC and Diffbind packages, Tom Carroll | BioC2014 | pdf, R | 2014‑07‑30 | 2.14/3.1.1 |
| Annotation | Accessing Annotation Resources, Martin Morgan | ISMB2014 | pdf, R, R | 2014‑07‑15 | 2.14/3.1.1 |
| RNASeq | Analysis of RNA-Seq Data, Mike Love | ISMB2014 | html | 2014‑07‑15 | 2.14/3.1.1 |
| Scalable Computing | Scalable Integrative Bioinformatics with Bioconductor, Vincent Carey | ISMB2014 | pptx | 2014‑07‑15 | 2.14/3.1.1 |
| R/Bioconductor | Trends in Genomic Data Analysis in R, Levi Waldron | ISMB2014 | 2014‑07‑15 | 2.14/3.1.1 | |
| Annotation | Annotations, Martin Morgan | useR2014 | html, R | 2014‑06‑30 | 2.14/3.1.0 |
| R/Bioconductor | Introduction to R / Bioconductor, Martin Morgan | useR2014 | html, R | 2014‑06‑30 | 2.14/3.1.0 |
| Data Representation | Sequence Data Representation, Martin Morgan | useR2014 | html, R | 2014‑06‑30 | 2.14/3.1.0 |
| RNASeq | Work flows : RNA-Seq, Martin Morgan | useR2014 | html, R | 2014‑06‑30 | 2.14/3.1.0 |
| Annotation | Annotations, Martin Morgan | SeattleFeb2014 | pdf, R, Rnw | 2014‑02‑27 | 2.14/3.1.0 |
| R/Bioconductor | Bioconductor - Slides, Martin Morgan | SeattleFeb2014 | pdf, Rnw, R | 2014‑02‑27 | 2.14/3.1.0 |
| Data Representation | Genomic Ranges - Slides, Martin Morgan | SeattleFeb2014 | pdf, Rnw, R | 2014‑02‑27 | 2.14/3.1.0 |
| Annotation | RNASeq Analysis, Martin Morgan | SeattleFeb2014 | pdf, Rnw, R | 2014‑02‑27 | 2.14/3.1.0 |
| RNASeq | Visualization of Genomic Data, Sonali Arora | SeattleFeb2014 | pdf, Rnw, R | 2014‑02‑27 | 2.14/3.1.0 |
| Visualization | Working with Annotations, Martin Morgan | SeattleFeb2014 | pdf, Rnw, R | 2014‑02‑27 | 2.14/3.1.0 |
| Data Representation | Working with DNA Sequences, Sonali Arora | SeattleFeb2014 | pdf, Rnw, R | 2014‑02‑27 | 2.14/3.1.0 |
| Genomic Ranges | Working with FASTQ, BAM, and VCF files, Martin Morgan | SeattleFeb2014 | pdf, Rnw, R | 2014‑02‑27 | 2.14/3.1.0 |
| Genomic Ranges | Working with Genomic Ranges, Martin Morgan | SeattleFeb2014 | pdf, Rnw, R | 2014‑02‑27 | 2.14/3.1.0 |
| R/Bioconductor | Working with R, Martin Morgan | SeattleFeb2014 | pdf, R, Rnw | 2014‑02‑27 | 2.14/3.1.0 |
| Annotation | Annotations, Martin Morgan | summerx | pdf, R, Rnw | 2014‑01‑27 | 2.14/3.1.0 |
| Best Practices | Best Practices for Managing R / Bioconductor Scripts, Martin Morgan | summerx | pdf, Rnw | 2014‑01‑27 | 2.14/3.1.0 |
| R/Bioconductor | Bioconductor, Martin Morgan | summerx | pdf, R, Rnw | 2014‑01‑27 | 2.14/3.1.0 |
| Genomic Ranges | Ranges, Hervé Pagès | summerx | pdf, R, Rnw | 2014‑01‑27 | 2.14/3.1.0 |
| Variants | Variants, Martin Morgan | summerx | pdf, Rnw | 2014‑01‑27 | 2.14/3.1.0 |
| Visualization | Visualization., Martin Morgan | summerx | pdf, R, Rnw | 2014‑01‑27 | 2.14/3.1.0 |
| RNASeq | A complete RNA-Seq differential expression workflow, Michael Love, Simon Anders, Wolfgang Huber | CSAMA2014 | pdf, R | 2014‑06‑22 | 2.14/3.1.1 |
| R/Bioconductor | Accessing resources - packages, classes, methods, and efficient code, Martin Morgan | CSAMA2014 | html, R | 2014‑06‑22 | 2.14/3.1.1 |
| ChIPSeq | ChIP-seq Analysis, Martin Morgan | CSAMA2014 | pdf, R | 2014‑06‑22 | 2.14/3.1.1 |
| Genomic Ranges | Computing with genomic ranges, sequences and alignments, Michael Lawrence | CSAMA2014 | 2014‑06‑22 | 2.14/3.1.1 | |
| DNASeq | DNA-Seq 1: Variant calling, Michael Lawrence | CSAMA2014 | 2014‑06‑22 | 2.14/3.1.1 | |
| DNASeq | DNA-Seq 2: visualisation and quality assessment of variant calls, Paul Theodor Pyl | CSAMA2014 | 2014‑06‑22 | 2.14/3.1.1 | |
| Statistics | Elements of statistics 1: t-test and linear model, Robert Gentleman | CSAMA2014 | 2014‑06‑22 | 2.14/3.1.1 | |
| Statistics | Elements of statistics 2: multiple testing, false discovery rates, independent filtering, Wolfgang Huber | CSAMA2014 | 2014‑06‑22 | 2.14/3.1.1 | |
| Statistics | Elements of statistics 3: Classification and clustering - basic concepts, Unknown | CSAMA2014 | html | 2014‑06‑22 | 2.14/3.1.1 |
| Statistics | Elements of statistics 4: regularisation & kernels, Wolfgang Huber | CSAMA2014 | 2014‑06‑22 | 2.14/3.1.1 | |
| Statistics | Elements of statistics 5: experimental design, Simon Anders | CSAMA2014 | 2014‑06‑22 | 2.14/3.1.1 | |
| Gene set enrichment | Gene set enrichment analysis, Robert Gentleman | CSAMA2014 | 2014‑06‑22 | 2.14/3.1.1 | |
| RNASeq | High-throughput sequencing: Alignment and related topic, Simon Anders | CSAMA2014 | 2014‑06‑22 | 2.14/3.1.1 | |
| Visualization | Image Analysis, Susan Holmes, Wolfgang Huber, Trevor Martin | CSAMA2014 | 2014‑06‑22 | 2.14/3.1.1 | |
| Introduction | Introduction to R and Bioconductor, Martin Morgan | CSAMA2014 | 2014‑06‑22 | 2.14/3.1.1 | |
| Proteomics | Proteomics, Laurent Gatto | CSAMA2014 | 2014‑06‑22 | 2.14/3.1.1 | |
| RNASeq | RNA-Seq 1: differential expression analysis - GLMs and testing, Simon Anders | CSAMA2014 | 2014‑06‑22 | 2.14/3.1.1 | |
| RNASeq | RNA-Seq 3: alternative exon usage, Alejandro Reyes | CSAMA2014 | 2014‑06‑22 | 2.14/3.1.1 | |
| Reporting | Reporting your analysis - authoring knitr/Rmarkdown, ReportingTools, shiny, Laurent Gatto | CSAMA2014 | pkg | 2014‑06‑22 | 2.14/3.1.1 |
| Variants | Variant tallies, visualisation, HDF5, Paul Theodor Pyl | CSAMA2014 | pdf, R | 2014‑06‑22 | 2.14/3.1.1 |
| Visualization | Visualisation in Statistical Genomics, Vincent Carey | CSAMA2014 | 2014‑06‑22 | 2.14/3.1.1 | |
| Annotation | Working with Ranges infrastructure: annotating and understanding regions, Martin Morgan | CSAMA2014 | pdf, R | 2014‑06‑22 | 2.14/3.1.1 |
| Annotation | Working with gene and genome annotations, Martin Morgan | CSAMA2014 | pdf, R | 2014‑06‑22 | 2.14/3.1.1 |
| eQTL / molecular-QTL | eQTL / molecular-QTL analyses, Vincent Carey | CSAMA2014 | 2014‑06‑22 | 2.14/3.1.1 |
Courses by year
Custom workshops
The Bioconductor project can provide customized workshops on statistical methods and software for the analysis of genomic data for different educational and industrial clients. Interested parties should contact Vincent Carey.