condiments
Differential Topology, Progression and Differentiation
Bioconductor version: 3.24 · Package version: 1.21.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("condiments")Details
| Maintainer | Hector Roux de Bezieux <hector.rouxdebezieux@berkeley.edu> |
| Author | Hector Roux de Bezieux [aut, cre] (ORCID: <https://orcid.org/0000-0002-1489-8339>), Koen Van den Berge [aut, ctb], Kelly Street [aut, ctb] |
| License | MIT + file LICENSE |
| URL | https://hectorrdb.github.io/condiments/index.html |
| Bug Reports | https://github.com/HectorRDB/condiments/issues |
| Downloads rank | 511 |
| Source branch | devel |
| biocViews | MultipleComparison, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
Documentation
- Generating toy datasets
- Overview of the condiments workflow
- More controls for the tests used in the condiments workflow
Download
Follow the installation instructions to use this package in your R session.
| Source package | condiments_1.21.0.tar.gz |
| Windows binary (x86_64) | condiments_1.21.0.zip |
| macOS binary (arm64) | condiments_1.21.0.tgz |
| macOS binary (x86_64) | condiments_1.21.0.tgz |
Dependencies
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
Suggests: knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN, DelayedMatrixStats