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.
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geneexpressiondifferentialexpressiongenesetenrichmentpathwayscpp
14.60 score 448 stars 54 dependents 6.6k scriptsmascarade - 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.
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7.09 score 45 stars 16 scripts 654 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.
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geneexpressiontranscriptomicsrnaseq
6.00 score 11 stars 1 dependents 9 scripts