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 5 days ago
geneexpressiondifferentialexpressiongenesetenrichmentpathways
369 stars 16.08 score 41 dependencies 102 dependentsphantasus - Visual and interactive gene expression analysis
Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.
Last updated 1 months ago
geneexpressionguivisualizationdatarepresentationtranscriptomicsrnaseqmicroarraynormalizationclusteringdifferentialexpressionprincipalcomponentimmunooncology
41 stars 7.72 score 155 dependenciesphantasusLite - 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 3 months ago
geneexpressiontranscriptomicsrnaseq
7 stars 6.23 score 34 dependencies 1 dependentsgatom - Finding an Active Metabolic Module in Atom Transition Network
This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization.
Last updated 5 months ago
geneexpressiondifferentialexpressionpathwaysnetwork
5 stars 5.48 score 109 dependencies