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The Top 23 Gene Expression Open Source Projects

Open source projects categorized as Gene Expression
Categories > Gene Expression
Awesome Single Cell ⭐ 2,784
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
most recent commit 3 months ago
Salmon ⭐ 661
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
most recent commit 8 months ago
Nichenetr ⭐ 416
NicheNet: predict active ligand-target links between interacting cells
most recent commit 3 months ago
Enformer Pytorch ⭐ 359
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
dependent packages 1total releases 98most recent commit 4 months agopypi enformer-pytorch} Downloads
Isee ⭐ 217
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
most recent commit 20 days ago
Tangram ⭐ 153
Spatial alignment of single cell transcriptomic data.
total releases 11most recent commit a year ago
Pymrmr ⭐ 135
Python3 binding to mRMR Feature Selection algorithm (currently not maintained)
dependent packages 1total releases 10most recent commit 4 months agopypi pymrmr} Downloads
D Gex ⭐ 117
Deep learning for gene expression inference
most recent commit 5 years ago
Clustergvis ⭐ 114
One-step to Cluster and Visualize Gene Expression Matrix
most recent commit 8 months ago
Awesome Expression Browser ⭐ 107
😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎
most recent commit a year ago
Tybalt ⭐ 107
Training and evaluating a variational autoencoder for pan-cancer gene expression data
most recent commit 5 years ago
Dorothea ⭐ 105
R package to access DoRothEA's regulons
most recent commit a year ago
Powsimr ⭐ 102
Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
most recent commit 9 months ago
Basics ⭐ 81
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version
most recent commit 4 months ago
Genetonic ⭐ 74
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
most recent commit 3 months ago
Epic ⭐ 68
Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.
most recent commit 9 months ago
Pancancer ⭐ 61
Building classifiers using cancer transcriptomes across 33 different cancer-types
most recent commit 5 years ago
Irap ⭐ 58
integrated RNA-seq Analysis Pipeline
most recent commit 5 years ago
Scope ⭐ 56
Fast visualization tool for large-scale and high dimensional single-cell data
most recent commit 2 years ago
Tf Bind Transformer ⭐ 45
A repository with exploration into using transformers to predict DNA ↔ transcription factor binding
total releases 94most recent commit 2 years ago
Biobombe ⭐ 44
BioBombe: Sequentially compressed gene expression features enhances biological signatures
most recent commit 3 years ago
Terminus ⭐ 43
most recent commit 2 years ago
Dgca ⭐ 38
Differential Gene Correlation Analysis
most recent commit 7 months ago
The 2 Most Depended On Gene Expression Open Source Projects
Pymrmr ⭐ 135
Python3 binding to mRMR Feature Selection algorithm (currently not maintained)
dependent packages 1total releases 10latest release January 28, 2021most recent commit 4 months agopypi pymrmr} Downloads
Enformer Pytorch ⭐ 359
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
dependent packages 1total releases 98latest release November 03, 2023most recent commit 4 months agopypi enformer-pytorch} Downloads
The 10 Latest Releases In Gene Expression Open Source Projects
Enformer Pytorch ⭐ 359
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
dependent packages 1total releases 98latest release November 03, 2023most recent commit 4 months agopypi enformer-pytorch} Downloads
Pinetree ⭐ 9
🌲 a flexible gene expression simulator with codon-specific translation rates
total releases 8latest release December 20, 2022most recent commit a year ago
Tejaas ⭐ 5
Tejaas - a tool for discovering trans-eQTLs
total releases 2latest release October 14, 2022most recent commit 2 years ago
Glmmseq ⭐ 15
Gene-level general linear mixed model
total releases 6latest release October 08, 2022most recent commit 2 years ago
Tangram ⭐ 153
Spatial alignment of single cell transcriptomic data.
total releases 11latest release June 17, 2022most recent commit a year ago
Glmmseq ⭐ 15
Gene-level general linear mixed model
total releases 2latest release March 30, 2021most recent commit 2 years ago
Mytai ⭐ 33
Evolutionary Transcriptomics with R
total releases 15latest release February 24, 2021most recent commit 7 months ago
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