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 27 days ago

geneexpressiondifferentialexpressiongenesetenrichmentpathways

16.21 score 379 stars 104 packages 3.9k scripts 27k downloads

phantasus - 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 27 days ago

geneexpressionguivisualizationdatarepresentationtranscriptomicsrnaseqmicroarraynormalizationclusteringdifferentialexpressionprincipalcomponentimmunooncology

7.75 score 42 stars 15 scripts 470 downloads

phantasusLite - 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 27 days ago

geneexpressiontranscriptomicsrnaseq

6.02 score 7 stars 1 packages 8 scripts 124 downloads

gatom - 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 27 days ago

geneexpressiondifferentialexpressionpathwaysnetwork

5.18 score 5 stars 8 scripts 127 downloads