Gene Set Enrichment Analysis and Over Representation Analysis analysis using R
-
Updated
Jun 20, 2019
#
gene-set-enrichment-analysis
Here are 16 public repositories matching this topic...
A high-performance variant of pre-ranked Gene Set Enrichment Analysis (GSEA) that is capable of testing gene sets where each gene has an expected direction of change from prior experiments.
-
Updated
Mar 31, 2026 - R
Transformer-based efficient and explainable gene set enrichment analysis
bioinformatics rna-seq transformer transcriptomics pathway-analysis explainable-ai transformer-architecture gene-set-enrichment-analysis saintgse
-
Updated
Apr 21, 2026 - Python
Itraa: A gene-set enrichment pipeline for selection and gene-based analyses.
-
Updated
Apr 24, 2025 - Python
Web application that enables users to compare the expression of genes or enrichment of gene sets between different molecular subtypes of colorectal cancer
gene-sets r shiny gene-expression enrichment-analysis gene-expression-signatures gsea pathway-enrichment-analysis gene-set-enrichment-analysis
-
Updated
Oct 18, 2023 - HTML
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…
bam-files rna-seq r script deseq2 rna-seq-analysis kegg wikipathways reactome ora geneontology gsea rna-seq-pipeline reactome-pathway differentially-expressed-genes clusterprofiler deseq2-analysis gene-set-enrichment-analysis diseaseontology over-rapresentation-analysis
-
Updated
Apr 14, 2023 - Jupyter Notebook
Role of CXCL9/10/11, CXCL13 and XCL1 in recruitment and suppression of cytotoxic T cells in renal cell carcinoma
cancer monte-carlo-simulation metabolism transcriptome renal immune tcell semi-supervised-clustering tumor-immunogenicity gene-set-enrichment-analysis immune-checkpoint
-
Updated
Mar 20, 2023 - R
Reproducible Snakemake pipeline for mouse astrocyte proteomics: differential abundance, g:Profiler GO/KEGG enrichment, REVIGO redundancy reduction, and small-n validation framework. Python, plotly, config-driven.
snakemake mass-spectrometry differential-expression pathway-enrichment-analysis proteomics-data-analysis gene-set-enrichment-analysis
-
Updated
Apr 15, 2026 - Python
An R package for DNA methylation data length bias adjustment in gene set testing
enrichment ontology methylation epigenetics logistic-regression dna-methylation differential-methylation enrichment-analysis generalized-linear-models ewas gene-set-enrichment-analysis
-
Updated
Dec 13, 2025 - R
Assessing the effectiveness of endocrine therapy in breast cancer using RNAseq data
-
Updated
Apr 19, 2022 - R
Nextflow DSL2 pipeline for sifting discovery proteomics data: QC, limma+DEqMS differential abundance, and enrichment feed an integrated per-protein profile database (UniProt, PubMed, DisGeNET, DGIdb, CTD) built for interactive exploration.
nextflow tool discovery exploratory-data-visualizations proteomics-data-analysis interactive-ui gene-set-enrichment-analysis
-
Updated
Apr 24, 2026 - Python
Expression, biological and clinical relevance of the collagen pathway genes in prostate carcinoma
survival-analysis signaling-pathways collagen differential-gene-expression metabolic-models prostate-cancer semi-supervised-clustering gradient-boosted-machines gene-ontology-terms gene-set-enrichment-analysis
-
Updated
Feb 26, 2024 - R
The Tasmanian devil is endangered due to Devil Facial Tumour Disease (DFTD), a contagious cancer with no current treatment. Previous study has investigated the anticancer properties of Tasmanian devil cathelicidins. This report intends to reproduce the enrichment analysis results of the study and further analyze their data.
bioinformatics rna-seq r cancer gene-expression gene-ontology edger limma gsea multidimensional-scaling gene-set-enrichment-analysis tasmanian-devil edaseq
-
Updated
Aug 6, 2024 - TeX
Gene set enrichment analysis from scRNA seq data : in search of the original tissue
-
Updated
Apr 19, 2022 - R
Snakemake pipeline to benchmark 11 functional pathway annotation systems
-
Updated
Jun 30, 2022 - Python
This repository contains code for identifying potential biomarkers of 2022 mpox virus using transcriptomic and machine learning analysis.
string machine-learning-algorithms pca-analysis deseq2 gene-ontology data-normalization rna-seq-analysis roc-curve tsne kegg-pathway umap limma differential-gene-expression scikitlearn-machine-learning random-forest-classifier ppi-networks microarray-data-analysis pycaret gene-set-enrichment-analysis feature-importance-analysis
-
Updated
Apr 10, 2025 - Jupyter Notebook
Improve this page
Add a description, image, and links to the gene-set-enrichment-analysis topic page so that developers can more easily learn about it.
Add this topic to your repo
To associate your repository with the gene-set-enrichment-analysis topic, visit your repo's landing page and select "manage topics."