transcriptomics

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

transcription-factors transcriptomics single-cell gene-regulatory-network

UpdatedJun 26, 2025
Python

mahmoodlab /PathomicFusion

Star311

Fusing Histology and Genomics via Deep Learning - IEEE TMI

genomics fusion transcriptomics pathology multimodal histopathology computational-pathogenomics pathomic multimodal-network mahmoodlab

UpdatedAug 22, 2022
Jupyter Notebook

theislab /scgen

Star309

Single cell perturbation prediction

bioinformatics deep-learning generative-model scrna-seq transcriptomics single-cell single-cell-genomics

UpdatedDec 5, 2024
Python

opencobra /cobratoolbox

Star263

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

tutorial metabolomics reconstruction transcriptomics cobra metabolic-models strain-engineering metabolic-reconstruction constraint-based-modeling microbiome-analysis metabolic-engineering gap-filling cobra-toolbox omics-data-integration human-metabolism

UpdatedJul 17, 2025
MATLAB

spacetx /starfish

Star234

starfish: unified pipelines for image-based transcriptomics

python transcriptomics imaging human-cell-atlas

UpdatedJul 3, 2025
Python

kharchenkolab /pagoda2

Star232

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

scrna-seq transcriptomics single-cell single-cell-rna-seq

UpdatedFeb 27, 2024
JavaScript

ZJUFanLab /scCATCH

Star230

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

rna-seq sequencing transcriptome transcriptomics single-cell marker-genes seurat cluster-annotation cell-markers

UpdatedMay 8, 2023
R

iSEE /iSEE

Star228

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

visualization gui shiny clustering gene-expression feature-extraction transcriptomics single-cell hacktoberfest dimension-reduction human-cell-atlas

UpdatedJul 8, 2025
R

scverse /decoupler

Star214

Python package to perform enrichment analysis from omics data.

python data-science bioinformatics enrichment numba transcriptomics single-cell enrichment-analysis spatial-transcriptomics

UpdatedJul 18, 2025
Python

GoekeLab /bambu

Star212

Reference-guided transcript discovery and quantification for long read RNA-Seq data

rna-seq r nanopore bioconductor transcriptomics rna-seq-analysis transcript-quantification bambu long-reads nanopore-sequencing transcript-reconstruction

UpdatedJun 27, 2025
R

keller-mark /awesome-biological-visualizations

Star201

A list of web-based interactive biological data visualizations.

visualization awesome medicine genomics cancer biology data-visualization awesome-list transcriptomics

UpdatedApr 2, 2024

theislab /diffxpy

Star199

Differential expression analysis for single-cell RNA-seq data.

bioinformatics tensorflow transcriptomics gene-set-enrichment differential-expression single-cell-rna-seq

UpdatedFeb 25, 2025
Python

COMBINE-lab /alevin-fry

Star189

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

rust rna-seq quantification transcriptomics single-cell 10x single-cell-rna-seq