msigdbr - MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
Provides the 'Molecular Signatures Database' (MSigDB) gene sets typically used with the 'Gene Set Enrichment Analysis' (GSEA) software (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>, Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>, Castanza et al. 2023 <doi:10.1038/s41592-023-02014-7>) as an R data frame. The package includes the human genes as listed in MSigDB as well as the corresponding symbols and IDs for frequently studied model organisms such as mouse, rat, pig, fly, and yeast.
Last updated 7 days ago
enrichment-analysisgene-setsgenomicsgseamsigdbpathway-analysispathways
12.20 score 73 stars 20 dependents 3.6k scripts 11k downloadsbabelgene - Gene Orthologs for Model Organisms in a Tidy Data Format
Genomic analysis of model organisms frequently requires the use of databases based on human data or making comparisons to patient-derived resources. This requires harmonization of gene names into the same gene space. The 'babelgene' R package converts between human and non-human gene orthologs/homologs. The package integrates orthology assertion predictions sourced from multiple databases as compiled by the HGNC Comparison of Orthology Predictions (HCOP) (Wright et al. 2005 <doi:10.1007/s00335-005-0103-2>, Eyre et al. 2007 <doi:10.1093/bib/bbl030>, Seal et al. 2011 <doi:10.1093/nar/gkq892>).
Last updated 2 years ago
8.00 score 12 stars 24 dependents 29 scripts 8.0k downloadsclustermole - Unbiased Single-Cell Transcriptomic Data Cell Type Identification
Assignment of cell type labels to single-cell RNA sequencing (scRNA-seq) clusters is often a time-consuming process that involves manual inspection of the cluster marker genes complemented with a detailed literature search. This is especially challenging when unexpected or poorly described populations are present. The clustermole R package provides methods to query thousands of human and mouse cell identity markers sourced from a variety of databases.
Last updated 1 years ago
cell-typecell-type-annotationcell-type-classificationcell-type-identificationcell-type-matchinggene-expression-signaturesscrna-seqsingle-cell
5.37 score 13 stars 36 scripts 535 downloadscopynumber - Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).
Penalized least squares regression is applied to fit piecewise constant curves to copy number data to locate genomic regions of constant copy number. Procedures are available for individual segmentation of each sample, joint segmentation of several samples and joint segmentation of the two data tracks from SNP-arrays. Several plotting functions are available for visualization of the data and the segmentation results.
Last updated 2 years ago
acghsnpcopynumbervariationgeneticsvisualization
3.88 score 19 stars 80 scriptsscooter - Streamlined scRNA-Seq Analysis Pipeline
Streamlined scRNA-Seq analysis pipeline.
Last updated 1 years ago
2.51 score 4 stars 16 scriptsphenomenalist - Analysis Toolkit for PhenoCycler (CODEX) Data in R
A collection of tools for cleaning, clustering, and plotting PhenoCycler (CODEX) data.
Last updated 1 years ago
codexphenocycler
2.18 score 3 stars 1 scriptsmsigdbdf - MSigDB Data Frame
Provides the Molecular Signatures Database (MSigDB) gene sets (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>, Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>, Castanza et al. 2023 <doi:10.1038/s41592-023-02014-7>) in an R data frame. Serves as the data source for 'msigdbr' <doi:10.32614/CRAN.package.msigdbr> (split into a separate package due to CRAN size restrictions).
Last updated 2 months ago
1.78 score 1 stars 1 scriptsvarnisch - What the Package Does (One Line, Title Case)
What the package does (one paragraph).
Last updated 1 years ago
1.70 score