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condiments

This is the development version of condiments; for the stable release version, see condiments.

Differential Topology, Progression and Differentiation

Bioconductor version: Development (3.18)

This package encapsulate many functions to conduct a differential topology analysis. It focuses on analyzing an 'omic dataset with multiple conditions. While the package is mostly geared toward scRNASeq, it does not place any restriction on the actual input format.

Author: Hector Roux de Bezieux [aut, cre] , Koen Van den Berge [aut, ctb], Kelly Street [aut, ctb]

Maintainer: Hector Roux de Bezieux <hector.rouxdebezieux at berkeley.edu>

Citation (from within R, enter citation("condiments")):

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("condiments")

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("condiments")
Generating more examples HTML R Script
The condiments workflow HTML R Script
Using condiments HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews MultipleComparison, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.9.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License MIT + file LICENSE
Depends R (>= 4.0)
Imports slingshot(>= 1.9), mgcv, RANN, stats, SingleCellExperiment, SummarizedExperiment, utils, magrittr, dplyr (>= 1.0), Ecume (>= 0.9.1), methods, pbapply, matrixStats, BiocParallel, TrajectoryUtils, igraph, distinct
Linking To
Suggests knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN
System Requirements
Enhances
URL https://hectorrdb.github.io/condiments/index.html
Bug Reports https://github.com/HectorRDB/condiments/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package condiments_1.9.0.tar.gz
Windows Binary condiments_1.9.0.zip
macOS Binary (x86_64) condiments_1.9.0.tgz
macOS Binary (arm64) condiments_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/condiments
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/condiments
Bioc Package Browser https://code.bioconductor.org/browse/condiments/
Package Short Url https://bioconductor.org/packages/condiments/
Package Downloads Report Download Stats