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>) in a standard R data frame with key-value pairs. 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 2 years ago

enrichment-analysisgene-setsgenomicsgseamsigdbpathway-analysispathways

11.96 score 70 stars 22 packages 2.8k scripts 7.1k 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>).

Last updated 2 years ago

7.87 score 11 stars 28 packages 24 scripts 6.6k 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.

Last updated 7 months ago

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

5.82 score 13 stars 34 scripts 480 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.

Last updated 2 years ago

acghsnpcopynumbervariationgeneticsvisualization

3.84 score 18 stars 77 scripts

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

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

Last updated 9 months ago

codexphenocycler

2.65 score 3 stars 1 scripts

scooter - Streamlined scRNA-Seq Analysis Pipeline

Streamlined scRNA-Seq analysis pipeline.

Last updated 1 years ago

2.30 score 4 stars 2 scripts

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

What the package does (one paragraph).

Last updated 8 months ago

1.70 score