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
14.21 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.
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cpp
7.74 score 46 stars 1 dependents 20 scripts 442 downloadsphantasus - 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.
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geneexpressionguivisualizationdatarepresentationtranscriptomicsrnaseqmicroarraynormalizationclusteringdifferentialexpressionprincipalcomponentimmunooncology
7.48 score 45 stars 24 scripts 594 downloadsgatom - 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.
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geneexpressiondifferentialexpressionpathwaysnetwork
6.10 score 8 stars 21 scripts 430 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
6.04 score 11 stars 1 dependents 11 scripts 318 downloadsrhdf5client - Access HDF5 content from HDF Scalable Data Service
This package provides functionality for reading data from HDF Scalable Data Service from within R. The HSDSArray function bridges from HSDS to the user via the DelayedArray interface. Bioconductor manages an open HSDS instance graciously provided by John Readey of the HDF Group.
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dataimportsoftwareinfrastructure
4.48 score 2 dependents 544 downloads