Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: gsea
DBRetina/DBRetina
DBRetina python package
Language: C++ - Size: 19.7 MB - Last synced: 1 day ago - Pushed: 4 days ago - Stars: 1 - Forks: 1
stemangiola/tidybulk
Brings bulk and pseudobulk transcriptomics to the tidyverse
Language: R - Size: 97.2 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 159 - Forks: 23
YuLab-SMU/clusterProfiler
:bar_chart: A universal enrichment tool for interpreting omics data
Language: R - Size: 15.1 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 947 - Forks: 245
moritzmadern/BulkRNAseqAnalysis_from_countMatrix
R Markdown script to perform bioinformatic analysis on RNA-seq raw count matrices, including DE-testing via DESeq2 and gene set enrichment analysis (GSEA).
Language: R - Size: 42.6 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 2 - Forks: 0
KwatMDPhD/GSEA.jl
The official command-line program for gene-set-enrichment analysis (GSEA) ๐๏ธ
Language: Julia - Size: 180 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 21 - Forks: 2
nf-core/differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
Language: Nextflow - Size: 7.77 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 45 - Forks: 24
zqfang/GSEApy
Gene Set Enrichment Analysis in Python
Language: Python - Size: 99 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 506 - Forks: 114
lianos/sparrow
Take command of your set enrichment analyses.
Language: R - Size: 398 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 20 - Forks: 1
guokai8/richR
Function Enrichment analysis and Network construction
Language: R - Size: 3.09 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 6 - Forks: 4
PathVisio/GSEA-plugin
GSEA plugin for PathVisio
Language: Java - Size: 3.35 MB - Last synced: about 2 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 1
igordot/msigdbr
MSigDB gene sets for multiple organisms in a tidy data format
Language: R - Size: 62.3 MB - Last synced: 17 days ago - Pushed: about 1 year ago - Stars: 64 - Forks: 12
krassowski/gsea-api
Pandas API for multiple Gene Set Enrichment Analysis implementations in Python (GSEApy, cudaGSEA, GSEA)
Language: Python - Size: 162 KB - Last synced: 9 days ago - Pushed: about 1 year ago - Stars: 14 - Forks: 2
broadinstitute/ssGSEA2.0
Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
Language: R - Size: 28.8 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 211 - Forks: 71
ToledoEM/msigdf Fork of stephenturner/msigdf
Molecular Signatures Database (MSigDB) in a data frame
Language: HTML - Size: 239 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 21 - Forks: 6
awakenedhaki/weaver
Gene set enrichment network visualization
Language: R - Size: 30.3 KB - Last synced: 3 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 0
JEFworks/liger
Lightweight Iterative Gene set Enrichment in R
Language: R - Size: 8.25 MB - Last synced: 20 days ago - Pushed: over 2 years ago - Stars: 55 - Forks: 11
genescf/GeneSCF
Gene Set Clustering based on Functional annotation
Language: Perl - Size: 4.53 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 21 - Forks: 5
CSBiology/TMEA
Thermodynamically Motivated Enrichment Analysis (TMEA) is a new approach to gene set enrichment analysis.
Language: F# - Size: 10.6 MB - Last synced: 22 days ago - Pushed: over 1 year ago - Stars: 8 - Forks: 3
NicolasH2/gggsea
GSEA plots in ggplot2
Language: R - Size: 1.1 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 6 - Forks: 4
chunjie-sam-liu/GSCA
An integrated genomic and immunogenomic web-based platform for gene set cancer research
Language: TypeScript - Size: 72.8 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0
mcrewcow/RGC_Dnmt3a_pONC2d_paper
Retinal ganglion cells regeneration in 2 days post optic nerve crush retina | Lydia Tai | Dong Feng Chen Lab collaboration | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School
Language: R - Size: 84 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 1
mcrewcow/BaranovLab
Main projects during my current position in Petr Baranov Lab | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School
Language: Jupyter Notebook - Size: 64.9 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 1 - Forks: 1
kerseviciute/aPEAR
Enrichment Networks for Pathway Enrichment Analysis
Language: R - Size: 4.99 MB - Last synced: 6 months ago - Pushed: about 1 year ago - Stars: 14 - Forks: 4
KILBAHA/Neuroblastoma-Transcriptomic-Analysis
Analysis of Neuroblastoma cancer patients to analyse their susceptibility to SARS-CoV-2. This research was conducted as a part of a group project during our Bioinformatics and Theoretical Systems Biology MSc at Imperial College London.
Language: Jupyter Notebook - Size: 598 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
MolecularPathologyLab/SubtypeExploreR
Web application that enables users to compare the expression of genes or enrichment of gene sets between different molecular subtypes of colorectal cancer
Language: HTML - Size: 950 KB - Last synced: 4 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0
matteocereda/GSECA
Gene Set Enrichment Class Analysis for heterogeneous RNA sequencing data
Language: R - Size: 56.4 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 5 - Forks: 0
ACastanza/seqformat
RNA-seq Preprocessing for GSEA
Language: R - Size: 6.04 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0
ilwookkim/Goheatmap
Heatmap with Gene Set Enrichment Analysis
Language: R - Size: 3.64 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0
LeRicNet/R-Scripts
repo for various R-based tools
Language: R - Size: 7.81 KB - Last synced: 7 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0
kn-bibs/pathways-analysis
Testing, development environment for a new project of KN BIBS
Language: Python - Size: 147 KB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 2 - Forks: 10
ameya225/useful_functions
Useful R functions
Language: R - Size: 21.5 KB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0
aprezvykh/bioinformatics
some scripts to process transcriptomics and Chip-seq data
Language: R - Size: 183 MB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 1 - Forks: 1
suhasvasaikar/GSEA_PHP
Gene set enrichment analysis with PHP
Language: PHP - Size: 13.9 MB - Last synced: 7 months ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0
raqmejtru/BCH339N_Predicting_Tumor_Phenotypes_from_Gene_Expression
We use gene expression data to perform gene set enrichments and random forest predictions to distinguish between four tumor types.
Language: R - Size: 28.5 MB - Last synced: 8 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0
raqmejtru/mitonuclear-sd
Investigate the role of mtDNA in the sex determination/development of Potamilus streckersoni, a freshwater mussel with doubly uniparental mitochondrial inheritance. Scripts for DESeq2, WGCNA, GSEA, AlphaFold/AlphaPulldown, and mt-sncRNA validation.
Language: R - Size: 91.8 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 1
nasqar/ClusterProfShinyGSEA
A web-based application to perform Gene Set Enrichment Analysis (GSEA) using clusterProfiler and shiny R libraries
Language: R - Size: 1.96 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 15 - Forks: 8
NKI-CCB/flexgsea-r
Flexible gene set enrichment analysis
Language: R - Size: 90.8 KB - Last synced: 6 days ago - Pushed: over 2 years ago - Stars: 10 - Forks: 2
noamteyssier/idea
Integrated Differential Expression and Annotation
Language: HTML - Size: 2.63 MB - Last synced: 22 days ago - Pushed: 7 months ago - Stars: 3 - Forks: 0
guhjy/GSEAMA Fork of dgrtwo/GSEAMA
Gene Set Enrichment Analysis Made Awesome
Language: R - Size: 463 KB - Last synced: 9 months ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0
RabbltMan/SimplePlotForGSEA
ๆ็ฎ็ใๅธฆๆUI็้ข็GSEAๅพ่กจ็ๆ่ๆฌใ
Language: Python - Size: 7.81 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0
genepattern/GSEA2
Module for GSEA Julia Implementation
Language: HTML - Size: 9.82 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0
serrano-pozo-lab/GFAP-OE-GSEA
GFAP overexpression GSEA results.
Language: HTML - Size: 167 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0
albertme0308/GSApp
GSApp Pathway Analysis
Language: HTML - Size: 10.2 MB - Last synced: 4 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0
IbrahimElzahaby/MSc_Thesis
Computational protemics analysis of cancer cell-lines at the level of single-cells
Language: R - Size: 104 MB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 1 - Forks: 0
alex-trapp/sc-fgsea
Automated tool for single-cell cluster annotation running on the fGSEA framework
Size: 654 KB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0
raulsanzr/GSEA
Gene set enrichment analysis workflows.
Size: 122 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0
francescopatane96/RNA-seq_Pipeline
Deposited R scripts allow to execute a complete RNA-seq Pipeline, starting from sequence reads (FASTQ files) to mapping/annotate the genome using a reference, to counts the number of reads for every gene. when raw counts are obtained, DESeq2 module permits to find differentially expressed genes (DEG) and to perform statistical analysis. The last module of the project allows you to use clusterprofiler in order to perform ORA and GSEA analysis (over-representation analysis and gene set enrichment analysis) using GeneOntology (GO), disease ontology (DO), KEGG, reactome eg...
Language: Jupyter Notebook - Size: 31.3 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0
xzhoulab/iDEA
Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)
Language: C++ - Size: 21.2 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 26 - Forks: 9
ArataHayashi/GENI-Gene-ENrichment-Identifier
Gene Enrichment Identifier
Language: R - Size: 152 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0
xpbowler/RNA-seq-data-analysis-
GSEA of HCV-RNAseq data
Language: HTML - Size: 3.53 MB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0
shbrief/GenomicSuperSignature
Interpretation of RNAseq experiments through robust, efficient comparison to public databases
Language: R - Size: 194 MB - Last synced: 6 months ago - Pushed: about 1 year ago - Stars: 12 - Forks: 7
gencorefacility/r-notebooks
Gene Set Enrichment Analysis and Over Representation Analysis analysis using R
Size: 1.33 MB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 11 - Forks: 23
kirushka/Tat_in_B_cells
Differential gene expression and gene enrichment analyses of B-cell line with ectopic expression of HIV-1 Tat protein
Language: R - Size: 72.3 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
ahalfpen727/Gene-Expression-SecondaRy-Analysis
Repository of R scripts for analysis of gene expression data
Language: R - Size: 99.9 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0
shawlab-moffitt/DRPPM-PreRanked-GSEA
As part of the DRPPM-PATH-SURVEIOR family, this R Shiny app aims to perform GSEA with a pre-ranked set of genes determined by hazard ratio
Language: R - Size: 51.3 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
NicolasH2/gseaCondenser
condense GSEA terms
Language: R - Size: 1.16 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0
ACastanza/GSEA_R_old
Revisions to the GSEA-P R Application (Subramanian and Tamayo et al 2005)
Language: R - Size: 10.6 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 1