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The Top 23 Python Transcriptomics Open Source Projects

Open source projects categorized as Python 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
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
Starfish ⭐ 220
starfish: unified pipelines for image-based transcriptomics
dependent packages 1total releases 48most recent commit 5 months agopypi starfish} Downloads
Scgen ⭐ 215
Single cell perturbation prediction
dependent packages 2total releases 9most recent commit 7 months agopypi scgen} Downloads
Diffxpy ⭐ 157
Differential expression analysis for single-cell RNA-seq data.
most recent commit a year ago
Xpore ⭐ 122
Identification of differential RNA modifications from nanopore direct RNA sequencing
total releases 20most recent commit 5 months ago
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
Isoquant ⭐ 98
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
most recent commit 3 months ago
Pychopper ⭐ 74
A tool to identify, orient, trim and rescue full length cDNA reads
most recent commit 2 years ago
Dammit ⭐ 69
just annotate it, dammit!
most recent commit 3 years ago
Cellxgene Gateway ⭐ 40
Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
dependent packages 1total releases 17most recent commit 9 months agopypi cellxgene-gateway} Downloads
Pyrovelocity ⭐ 31
𝒫robabilistic modeling of RNA velocity ⬱
total releases 3most recent commit 4 months ago
Pisces ⭐ 26
PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
total releases 15most recent commit 9 months ago
Teaching ⭐ 25
This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.
most recent commit 3 months ago
Chromoformer ⭐ 24
The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
total releases 4most recent commit 8 months ago
Nmdc Schema ⭐ 23
This repository contains the LinkML specification for the NMDC schema and the artifacts generated by LinkML.
dependent packages 1total releases 70most recent commit 3 months agopypi nmdc-schema} Downloads
Pipeline Pinfish Analysis ⭐ 22
Pipeline for annotating genomes using long read transcriptomics data with pinfish
most recent commit 3 years ago
Elvers ⭐ 21
(formerly eelpond) an automated RNA-Seq workflow system
most recent commit 4 years ago
Pipeline Nanopore Denovo Isoforms ⭐ 19
Pipeline for de novo clustering of long transcriptomic reads
most recent commit 2 years ago
Rnaseq Pipeline ⭐ 18
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
most recent commit 3 months ago
Enrich_omics ⭐ 15
A python package to explore pathways, diseases and drugs associated to a list of targets (genes, proteins, etc)
most recent commit 4 months ago
The 9 Most Depended On Python 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
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
Scgen ⭐ 215
Single cell perturbation prediction
dependent packages 2total releases 9latest release April 25, 2022most recent commit 7 months agopypi scgen} 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
Stabilized Ica ⭐ 12
This repository proposes a python implementation of a stabilized ICA algorithm
dependent packages 1total releases 4latest release December 22, 2021most recent commit a year agopypi stabilized-ica} Downloads
Nmdc Schema ⭐ 23
This repository contains the LinkML specification for the NMDC schema and the artifacts generated by LinkML.
dependent packages 1total releases 70latest release June 16, 2022most recent commit 3 months agopypi nmdc-schema} Downloads
Starfish ⭐ 220
starfish: unified pipelines for image-based transcriptomics
dependent packages 1total releases 48latest release May 03, 2021most recent commit 5 months agopypi starfish} Downloads
The 10 Latest Releases In Python 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
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
Pyrovelocity ⭐ 31
𝒫robabilistic modeling of RNA velocity ⬱
total releases 3latest release September 06, 2023most recent commit 4 months ago
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
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