gene-modules

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parashardhapola /scarf

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

bioinformatics big-data genomics clustering scrna-seq graph-analytics memory-efficient tsne differential-expression umap dimension-reduction single-cell-genomics single-cell-rna-seq scalable-data-analysis single-cell-atac-seq multiomics cite-seq pseudotime scatac-seq gene-modules

UpdatedNov 19, 2025
Python

carmonalab /pyucell

Star15

Robust and scalable single-cell signature scoring

python signatures single-cell gene-modules

UpdatedFeb 11, 2026
Python

greenelab /phenoplier

Star15

PhenoPLIER

tool software unsupervised-learning complex-traits twas gene-modules

UpdatedApr 8, 2024
Jupyter Notebook

greenelab /phenoplier_manuscript

Star1

PhenoPLIER manuscript

manuscript unsupervised-learning complex-traits manubot gene-modules

UpdatedJul 29, 2024
TeX

camilababo /BIONIC

Star0

This repository contains MSc thesis results using BIONIC (developed by Duncan Forster at The University of Toronto) for the prediction of Arabidopsis's temperature-responsive gene modules.

deep-learning arabidopsis-thaliana gene-modules