fgsea - Fast Gene Set Enrichment Analysis
The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.
Last updated
geneexpressiondifferentialexpressiongenesetenrichmentpathwayscpp
14.21 score 459 stars 57 dependents 38 scripts 60k downloadsmascarade - Generating Cluster Masks for Single-Cell Dimensional Reduction Plots
Implements a procedure to automatically generate 2D masks for clusters on dimensional reduction plots from methods like t-SNE (t-distributed stochastic neighbor embedding) or UMAP (uniform manifold approximation and projection), with a focus on single-cell RNA-sequencing data.
Last updated
cpp
7.74 score 46 stars 1 dependents 20 scripts 442 downloadsphantasusLite - Loading and annotation RNA-seq counts matrices
PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects.
Last updated
geneexpressiontranscriptomicsrnaseq
6.04 score 11 stars 1 dependents 11 scripts 318 downloads