Projects in Awesome Lists tagged with differential-expression

https://github.com/owkin/PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

bioinformatics differential-expression python rna-seq transcriptomics

Last synced: 09 May 2025

https://github.com/tidyomics/tidybulk

Brings bulk and pseudobulk transcriptomics to the tidyverse

bioconductor bulk-transcriptional-analyses deseq2 differential-expression edger ensembl-ids entrez gene-symbols gsea mds-dimensions pca pipe redundancy tibble tidy tidy-data tidyverse transcriptomics transcripts tsne

Last synced: 21 Feb 2026

https://github.com/saeyslab/multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

cell-cell-communication cell-cell-interaction differential-expression intercellular-communication intercellular-signaling ligand-receptor ligand-receptor-interaction ligand-target scrna-seq single-cell single-cell-rna-seq systems-biology

Last synced: 26 Feb 2026

https://github.com/wckdouglas/diffexpr

Porting DESeq2 into python via rpy2

differential-expression python rna-seq

Last synced: 11 Apr 2025

https://baderlab.github.io/scClustViz/

Explore and share your scRNAseq clustering results

clustering-evaluation differential-expression r scrna-seq scrna-seq-analysis scrnaseq shiny single-cell ui

Last synced: 15 Nov 2025

https://github.com/baderlab/scclustviz

Explore and share your scRNAseq clustering results

clustering-evaluation differential-expression r scrna-seq scrna-seq-analysis scrnaseq shiny single-cell ui

Last synced: 04 Apr 2025

https://github.com/mritchielab/glimmav2

interactive plots for differential expression analysis

differential-expression interactive-visualizations r

Last synced: 21 Feb 2026

https://github.com/noamteyssier/adpbulk

pseudobulking on an AnnData object

anndata differential-expression pseudobulk scanpy

Last synced: 18 Jan 2026

https://github.com/federicomarini/ideal

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

bioconductor differential-expression r reproducible-research rna-seq rna-seq-analysis shiny user-friendly

Last synced: 06 Apr 2025

https://github.com/theislab/batchglm

Fit generalized linear models in python.

differential-expression generalized-linear-models tensorflow

Last synced: 11 Oct 2025

https://github.com/lpantano/degreport

Create a cromphensive report of DEG list coming from any analysis of RNAseq data

bioconductor differential-expression qc r report rna-seq smallrna

Last synced: 17 Mar 2025

https://github.com/hemberg-lab/d3e

Discrete Distributional Differential Expression

differential-expression human-cell-atlas single-cell-rna-seq

Last synced: 13 Apr 2025

https://github.com/lingfeiwang/normalisr

Causal inference, differential expression, and co-expression for scRNA-seq

association-testing causal-inference co-expression differential-expression gene-regulatory-network hypothesis-testing normalization scrna-seq single-cell single-cell-crispr-screening

Last synced: 03 Aug 2025

https://github.com/fperraudeau/singlecellworkflow

Tutorial for the analysis of scRNA-seq data in R

bioconductor clustering differential-expression dimensionality-reduction lineage normalization r single-cell single-cell-rna-seq workflow

Last synced: 12 Sep 2025

https://github.com/caranathunge/promor

A comprehensive R package for label-free proteomics data analysis and modeling

biomarkers differential-expression lfq machine-learning mass-spectrometry modeling proteomics r r-package rstats

Last synced: 24 Sep 2025

https://github.com/sing-group/my-brain-seq

myBrain-Seq: a Compi pipeline for miRNA-Seq data analysis in neuropsychiatry

compi differential-expression docker mirna mirna-seq pipeline

Last synced: 23 Feb 2026

https://github.com/bhklab/survcomp

R package for performance assessment and comparison for survival analysis

differential-expression gene-expression regression survival visualization

Last synced: 13 Apr 2025

https://github.com/inmegen/pipelines_inmegen

Flujos de trabajos desarrollados y automatizados en el Intituto Nacional de Medicina Genómica para el procesamiento de datos genómicos y transcriptómicos.

bioinformatics differential-expression dockerfile genomic-data-analysis nextflow-pipeline rnaseq-analysis somatic-variants transcriptome-analysis variant-calling

Last synced: 08 Apr 2026

https://github.com/poisonalien/beadanalyze

Automated differential expression analysis for Illumina beadarrays (HT12 V4 arrays).

differential-expression idat illumina-beadarrays microarry

Last synced: 12 May 2025

https://github.com/showteeth/debpeak

DEbPeak - Analyze and integrate multi-omics to unravel the regulation of gene expression.

analysis atac-seq chip-seq count-matrix differential-expression geo integration m6a-seq peak-related rna-seq transcription-factors visualization

Last synced: 01 Apr 2026

https://github.com/htpusa/moomin

MOOMIN is a tool for analysing differential expression data

constraint-based-modeling differential-expression gene-expression matlab metabolic-network moomin

Last synced: 13 Oct 2025

https://github.com/liuy12/scdeconr

Deconvolution of bulk RNA-seq data using single-cell RNA-seq data as reference

bulk-rna-seq-deconvolution deconvolution differential-expression ffpe geneset-enrichment-analysis r scdeconr single-cell

Last synced: 22 Oct 2025

https://github.com/kandarprj/epidecoder

Online version of tool is live

differential-expression epigenetics epitranscriptomics genomics genomics-visualization

Last synced: 31 Oct 2025

https://github.com/pentalpha/r-peridot

Software for intuitively doing Differential Gene Expression (DGE) analysis on Windows and GNU\Linux, based on R packages.

bioconductor bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-tool differential-expression differential-expression-analysis gene-expression rna-seq-analysis rna-seq-pipeline

Last synced: 15 May 2026

https://github.com/fjcamlab/deco

DECO :: Decomposing heterogeneous population cohorts for patient stratification and discovery of biomarkers using omic data profiling. R package

bioinformatics deco differential-expression heterogeneity heterogeneous-populations omic-data-profiling omics patients-stratification r sampling-methods stratification

Last synced: 19 Feb 2026

https://github.com/htpusa/moomin.jl

From differential gene expression to metabolic changes

constraint-based-modeling differential-expression gene-expression metabolic-models transcriptomics

Last synced: 11 Apr 2025

https://github.com/sing-group/dewe

DEWE (Differential Expression Workflow Executor) is an open source application for easily executing Differential Expression analyses in RNA-Seq data.

aibench differential-expression java rna-seq rna-seq-data rna-seq-pipeline

Last synced: 03 Jul 2025

https://github.com/pentalpha/r-peridot-gui

The power of the R's differential gene expression analysis packages, with no programming required.

bioinformatics bioinformatics-analysis bioinformatics-pipeline differential-expression genomics gui-application rna-seq rna-seq-analysis rna-seq-pipeline transcriptomics

Last synced: 15 May 2026

https://github.com/eweitz/degenome

Differential expression across the genome

differential-expression pipeline

Last synced: 03 Jul 2025

https://github.com/jaydu1/causarray

causarray is a Python module for simultaneous causal inference with an array of outcomes.

causal-inference differential-expression genomics single-cell unmeasured-confounding

Last synced: 01 Apr 2025

https://github.com/arnikz/emf_data_mining

Command-line tools in R/Python to analyze semi-quantitative mass spectrometry data on EMF exposures

bioinformatics-analysis differential-expression emf-exposures proteomics

Last synced: 04 Oct 2025

https://github.com/ayushnoori/nd-diff-expr

Differential gene expression data from the human central nervous system across Alzheimer’s disease, Lewy body diseases, and ALS-FTD.

differential-expression meta-analysis neurodegeneration transcriptomics

Last synced: 19 Feb 2026

https://github.com/jcaperella29/methylation_shiny

An interactive R Shiny web app for DNA methylation analysis with support for DE, pathway enrichment, power analysis, and machine learning — deployable on HPC via Singularity/Apptainer.

apptainer bioconductor bioinformatics data-visualization differential-expression epigenetics genomics machine-learning methylation pathway-enrichment-analysis pca r random-forest shiny singularity umap

Last synced: 02 Aug 2025

https://github.com/kgorze/rna-seq-nextflow

A reproducible, scalable, and containerized RNA-Seq analysis pipeline implemented in Nextflow. Features modular design with quality control (FastQC/MultiQC), alignment (STAR/HISAT2), quantification (Salmon/featureCounts), and differential expression analysis (DESeq2) components. Includes Docker containerization and CI/CD with GitHub Actions.

bioinformatics differential-expression docker nextflow pipeline rna-seq

Last synced: 24 Jan 2026

https://github.com/arunbodd/serum-proteomics

This repository Contains analysis pipeline for processing and analyzing mass spectrometry proteomics data

differential-expression mass-spectrometry

Last synced: 24 Jan 2026

https://github.com/genialis/shrnade

Part of shRNA pipeline.

bioinformatics differential-expression ngs shrna

Last synced: 26 Mar 2025

https://github.com/jcaperella29/differential-analysis-on-scrna-seq-data-in-r

using Seurat to perform DE analysis on scRNA seq data

bioinformatics-pipeline differential-expression seurat single-cell

Last synced: 19 Apr 2026

https://github.com/nowon1/scrna_seq_analysis

This repository contains an analysis pipeline for processing and visualizing single-cell RNA sequencing (scRNA-seq) data using the Seurat package in R. The dataset used is the Peripheral Blood Mononuclear Cells (PBMC) 3K dataset from 10X Genomics.

bioinformatics cell-clustering cell-type-annotation computational-biology data-analysis-in-r differential-expression dimensionality-reduction immunology integration marker-genes multimodal-integration normalization quality-control r-package scrna-seq seurat transcriptomics-data-integration