condiments

DOI: 10.18129/B9.bioc.condiments    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see condiments.

Differential Topology, Progression and Differentiation

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")

 

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

Details

biocViews	MultipleComparison, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.13 (R-4.1) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.1)
Imports	slingshot(>= 1.9), mgcv, RANN, stats, SingleCellExperiment, SummarizedExperiment, utils, magrittr, dplyr (>= 1.0), Ecume (>= 0.9.1), methods, pbapply, matrixStats, BiocParallel, TrajectoryUtils, igraph
LinkingTo
Suggests	knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN
SystemRequirements
Enhances
URL	https://hectorrdb.github.io/condiments/index.html
BugReports	https://github.com/HectorRDB/condiments/issues
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_1.0.0.tar.gz
Windows Binary	condiments_1.0.0.zip
macOS 10.13 (High Sierra)	condiments_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/condiments
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/condiments
Package Short Url	https://bioconductor.org/packages/condiments/
Package Downloads Report	Download Stats