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The Top 23 Bioinformatics Transcriptomics Open Source Projects

Open source projects categorized as Bioinformatics Transcriptomics
Categories > Data Processing > Bioinformatics
Categories > Transcriptomics
Scanpy ⭐ 1,753
Single-cell analysis in Python. Scales to >1M cells.
dependent packages 440total releases 77most recent commit 3 days agopypi scanpy} Downloads
Anndata ⭐ 495
Annotated data.
dependent packages 399total releases 78most recent commit 17 days agopypi anndata} Downloads
Pydeseq2 ⭐ 470
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
most recent commit 3 months ago
Scgen ⭐ 215
Single cell perturbation prediction
dependent packages 2total releases 9most recent commit 7 months agopypi scgen} Downloads
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
Pandora ⭐ 127
PANDORA Advanced Machine Learning for Data Integration, Analysis, and Insightful Discoveries in Health and Disease 💻
most recent commit 6 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
Rnalysis ⭐ 114
RNA sequencing analysis software
total releases 43most recent commit 4 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 4 months ago
Honeybadger ⭐ 94
HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
most recent commit 3 years ago
Dammit ⭐ 69
just annotate it, dammit!
most recent commit 3 years ago
Singlecellhaystack ⭐ 68
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
most recent commit 4 months ago
Cirrocumulus ⭐ 55
Bring your single-cell data to life
total releases 147most recent commit 5 months ago
Tomicsvis ⭐ 50
Transcriptomics Visualization R package.
total releases 1most recent commit 4 months ago
Dee2 ⭐ 37
Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data
most recent commit 8 months ago
Spatialtranscriptomics ⭐ 34
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
most recent commit 3 months ago
Metaomgraph ⭐ 30
MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets
most recent commit 2 years ago
Volcano3d ⭐ 28
An R package to plot interactive three-way differential expression analysis
total releases 1most recent commit 8 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
Mudskipper ⭐ 25
A tool for projecting genomic alignments to transcriptomic coordinates
total releases 1most recent commit 10 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
The 4 Most Depended On Bioinformatics Transcriptomics Open Source Projects
Scanpy ⭐ 1,753
Single-cell analysis in Python. Scales to >1M cells.
dependent packages 440total releases 77latest release October 31, 2023most recent commit 3 days agopypi scanpy} Downloads
Anndata ⭐ 495
Annotated data.
dependent packages 399total releases 78latest release October 31, 2023most recent commit 17 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
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 Bioinformatics Transcriptomics Open Source Projects
Rnalysis ⭐ 114
RNA sequencing analysis software
total releases 43latest release November 22, 2023most recent commit 4 months ago
Glue Genes ⭐ 7
glue for genomics and transcriptomics
total releases 7latest release November 22, 2023most recent commit 5 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 ⭐ 1,753
Single-cell analysis in Python. Scales to >1M cells.
dependent packages 440total releases 77latest release October 31, 2023most recent commit 3 days agopypi scanpy} Downloads
Anndata ⭐ 495
Annotated data.
dependent packages 399total releases 78latest release October 31, 2023most recent commit 17 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
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
Tomicsvis ⭐ 50
Transcriptomics Visualization R package.
total releases 1latest release July 06, 2023most recent commit 4 months ago
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