condiments
This is the development version of condiments; for the stable release version, see condiments.
Differential Topology, Progression and Differentiation
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Hector Roux de Bezieux <hector.rouxdebezieux at berkeley.edu>
citation("condiments")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | MultipleComparison, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
| Version | 1.15.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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 |
See More
| Suggests | knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN, DelayedMatrixStats |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | condiments_1.15.0.tar.gz |
| Windows Binary (x86_64) | condiments_1.15.0.zip |
| macOS Binary (x86_64) | condiments_1.15.0.tgz |
| macOS Binary (arm64) | |
| 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 |