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 2 months ago

geneexpressiondifferentialexpressiongenesetenrichmentpathwayscpp

16.25 score 387 stars 101 dependents 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 4 months ago

geneexpressionguivisualizationdatarepresentationtranscriptomicsrnaseqmicroarraynormalizationclusteringdifferentialexpressionprincipalcomponentimmunooncology

7.71 score 43 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 4 months ago

geneexpressiontranscriptomicsrnaseq

6.08 score 8 stars 1 dependents 8 scripts 170 downloads

mwcsr - Solvers for Maximum Weight Connected Subgraph Problem and Its Variants

Algorithms for solving various Maximum Weight Connected Subgraph Problems, including variants with budget constraints, cardinality constraints, weighted edges and signals. The package represents an R interface to high-efficient solvers based on relax-and-cut approach (Álvarez-Miranda E., Sinnl M. (2017) <doi:10.1016/j.cor.2017.05.015>) mixed-integer programming (Loboda A., Artyomov M., and Sergushichev A. (2016) <doi:10.1007/978-3-319-43681-4_17>) and simulated annealing.

Last updated 5 months ago

cplexcpp

5.98 score 7 stars 1 dependents 15 scripts 266 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 4 months ago

geneexpressiondifferentialexpressionpathwaysnetwork

5.18 score 5 stars 8 scripts 160 downloads