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>

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

Installation

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


if (!require("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")

Generating more examples HTML R Script

The condiments workflow HTML R Script

Using condiments HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews MultipleComparison, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization

Version 1.0.0

In Bioconductor since BioC 3.13 (R-4.1) (3 years)

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

System Requirements

URL https://hectorrdb.github.io/condiments/index.html

Bug Reports https://github.com/HectorRDB/condiments/issues

Suggests knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN

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