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.

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enrichment-analysisgene-setsgenomicsgseamsigdbpathway-analysispathways

12.69 score 84 stars 23 dependents 5.9k scripts 24k downloads

babelgene - 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>).

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8.90 score 15 stars 29 dependents 80 scripts 15k downloads

clustermole - 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.

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cell-typecell-type-annotationcell-type-classificationcell-type-identificationcell-type-matchinggene-expression-signaturesscrna-seqsingle-cell

5.47 score 15 stars 39 scripts 397 downloads

copynumber - 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.

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acghsnpcopynumbervariationgeneticsvisualization

4.03 score 21 stars 102 scripts

scooter - Streamlined scRNA-Seq Analysis Pipeline

Streamlined scRNA-Seq analysis pipeline.

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3.37 score 6 stars 79 scripts

msigdbrdata - 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).

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2.60 score 2 stars 2 scripts

altmem - Alternative Interface to cytoMEM Marker Enrichment Modeling

Automatically generate and display quantitative labels for cell populations that have been identified from flow cytometry, mass cytometry, and single-cell RNA-seq data.

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2.18 score 2 scripts

phenomenalist - Analysis Toolkit for PhenoCycler (CODEX) Data in R

A collection of tools for cleaning, clustering, and plotting PhenoCycler (CODEX) data.

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codexphenocycler

2.18 score 3 stars 3 scripts

varnisch - What the Package Does (One Line, Title Case)

What the package does (one paragraph).

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1.70 score