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The Top 23 Transcriptomics Open Source Projects

Open source projects categorized as Transcriptomics
Categories > Transcriptomics
Scanpy ⭐ 1,729
Single-cell analysis in Python. Scales to >1M cells.
dependent packages 440total releases 77most recent commit 14 days agopypi scanpy} Downloads
Cellxgene ⭐ 544
An interactive explorer for single-cell transcriptomics data
dependent packages 2total releases 41most recent commit 3 months agopypi cellxgene} Downloads
Anndata ⭐ 495
Annotated data.
dependent packages 399total releases 78most recent commit 10 days agopypi anndata} Downloads
Pydeseq2 ⭐ 470
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
most recent commit 3 months ago
Pyscenic ⭐ 321
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.
dependent packages 6total releases 63most recent commit 9 months agopypi pyscenic} Downloads
Cobratoolbox ⭐ 232
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
most recent commit 3 months ago
Starfish ⭐ 220
starfish: unified pipelines for image-based transcriptomics
dependent packages 1total releases 48most recent commit 5 months agopypi starfish} Downloads
Isee ⭐ 217
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
most recent commit 15 days ago
Scgen ⭐ 215
Single cell perturbation prediction
dependent packages 2total releases 9most recent commit 7 months agopypi scgen} Downloads
Pagoda2 ⭐ 186
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
dependent packages 3total releases 9most recent commit 2 months ago
Sccatch ⭐ 171
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
total releases 5most recent commit a year ago
Scde ⭐ 163
R package for analyzing single-cell RNA-seq data
most recent commit a year ago
Diffxpy ⭐ 157
Differential expression analysis for single-cell RNA-seq data.
most recent commit a year ago
Tidybulk ⭐ 153
Brings bulk and pseudobulk transcriptomics to the tidyverse
most recent commit 4 months ago
Bambu ⭐ 150
Reference-guided transcript discovery and quantification for long read RNA-Seq data
most recent commit 4 months ago
Pathomicfusion ⭐ 148
Fusing Histology and Genomics via Deep Learning - IEEE TMI
most recent commit 2 years ago
Pandora ⭐ 127
PANDORA Advanced Machine Learning for Data Integration, Analysis, and Insightful Discoveries in Health and Disease 💻
most recent commit 6 months ago
Cell Ontology ⭐ 126
An ontology of cell types
most recent commit 3 months ago
Dnanalyzer ⭐ 122
Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools
most recent commit 5 months ago
Xpore ⭐ 122
Identification of differential RNA modifications from nanopore direct RNA sequencing
total releases 20most recent commit 5 months ago
Alevin Fry ⭐ 115
🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
dependent packages 2total releases 10most recent commit 10 months agocargo libradicl} Downloads
Rnalysis ⭐ 114
RNA sequencing analysis software
total releases 43most recent commit 3 months ago
Decoupler Py ⭐ 112
Python package to perform enrichment analysis from omics data.
dependent packages 3total releases 10most recent commit 3 months agopypi decoupler} Downloads
The 10 Most Depended On Transcriptomics Open Source Projects
Scanpy ⭐ 1,729
Single-cell analysis in Python. Scales to >1M cells.
dependent packages 440total releases 77latest release October 31, 2023most recent commit 14 days agopypi scanpy} Downloads
Anndata ⭐ 495
Annotated data.
dependent packages 399total releases 78latest release October 31, 2023most recent commit 10 days agopypi anndata} Downloads
Decoupler Py ⭐ 112
Python package to perform enrichment analysis from omics data.
dependent packages 3total releases 10latest release August 31, 2023most recent commit 3 months agopypi decoupler} Downloads
Pagoda2 ⭐ 186
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
dependent packages 3total releases 9latest release December 12, 2021most recent commit 2 months ago
Cellxgene ⭐ 544
An interactive explorer for single-cell transcriptomics data
dependent packages 2total releases 41latest release September 21, 2022most recent commit 3 months agopypi cellxgene} Downloads
Scplot ⭐ 8
Single cell interactive plotting tools
dependent packages 2total releases 16latest release January 30, 2020most recent commit 4 years agopypi scplot} Downloads
Nease ⭐ 7
A network-based approach for exon set enrichment
dependent packages 2total releases 13latest release April 21, 2022most recent commit 2 years agopypi nease} Downloads
Scgen ⭐ 215
Single cell perturbation prediction
dependent packages 2total releases 9latest release April 25, 2022most recent commit 7 months agopypi scgen} Downloads
The 10 Latest Releases In Transcriptomics Open Source Projects
Rnalysis ⭐ 114
RNA sequencing analysis software
total releases 43latest release November 22, 2023most recent commit 3 months ago
Glue Genes ⭐ 7
glue for genomics and transcriptomics
total releases 7latest release November 22, 2023most recent commit 4 months ago
Curare ⭐ 6
Curare - A customizable and reproducible analysis pipeline for RNA-Seq experiments
total releases 5latest release November 16, 2023most recent commit 5 months ago
Discbio ⭐ 9
A user-friendly R pipeline for biomarker discovery in single-cell transcriptomics
total releases 6latest release November 06, 2023most recent commit 5 months ago
Scanpy ⭐ 1,729
Single-cell analysis in Python. Scales to >1M cells.
dependent packages 440total releases 77latest release October 31, 2023most recent commit 14 days agopypi scanpy} Downloads
Anndata ⭐ 495
Annotated data.
dependent packages 399total releases 78latest release October 31, 2023most recent commit 10 days agopypi anndata} Downloads
Cirrocumulus ⭐ 55
Bring your single-cell data to life
total releases 147latest release September 29, 2023most recent commit 5 months ago
Sandy ⭐ 14
A straightforward and complete next-generation sequencing read simulator
total releases 9latest release September 19, 2023most recent commit 5 months ago
Pyrovelocity ⭐ 31
𝒫robabilistic modeling of RNA velocity ⬱
total releases 3latest release September 06, 2023most recent commit 4 months ago
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