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Differential Topology, Progression and Differentiation

Bioconductor version: Release (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")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews MultipleComparison, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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
System Requirements
URL https://hectorrdb.github.io/condiments/index.html
Bug Reports https://github.com/HectorRDB/condiments/issues
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Suggests knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN
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Package Archives

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

Source Package condiments_1.10.0.tar.gz
Windows Binary condiments_1.10.0.zip
macOS Binary (x86_64) condiments_1.10.0.tgz
macOS Binary (arm64) condiments_1.10.0.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/
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