NanoporeRNASeq
This is the development version of NanoporeRNASeq; for the stable release version, see NanoporeRNASeq.
Nanopore RNA-Seq Example data
Bioconductor version: Development (3.18)
The NanoporeRNASeq package contains long read RNA-Seq data generated using Oxford Nanopore Sequencing. The data consists of 6 samples from two human cell lines (K562 and MCF7) that were generated by the SG-NEx project. Each of these cell lines has three replicates, with 1 direct RNA sequencing data and 2 cDNA sequencing data. Reads are aligned to chromosome 22 (Grch38) and stored as bam files. The original data is from the SG-NEx project.
Author: Jonathan Goeke [aut], Ying Chen [cre], Yuk Kei Wan [aut]
Maintainer: Ying Chen <chen_ying at gis.a-star.edu.sg>
citation("NanoporeRNASeq")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("NanoporeRNASeq")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("NanoporeRNASeq")| NanoporeRNASeq | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ExperimentData, ExperimentHub, Genome, RNASeqData, SequencingData |
| Version | 1.11.0 |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.0.0), ExperimentHub(>= 1.15.3) |
| Imports | |
| Linking To | |
| Suggests | knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize, ComplexHeatmap, apeglm, rlang, rmarkdown, GenomicAlignments, Rsamtools |
| System Requirements | |
| Enhances | parallel |
| URL | https://github.com/GoekeLab/NanoporeRNASeq |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | bambu |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | NanoporeRNASeq_1.11.0.tar.gz |
| Windows Binary | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/NanoporeRNASeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/NanoporeRNASeq |
| Package Short Url | https://bioconductor.org/packages/NanoporeRNASeq/ |
| Package Downloads Report | Download Stats |