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clin-oracle-tahoe-hack-2025 Public
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PyDESeq2 Public
Forked from owkin/PyDESeq2A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
Python MIT License UpdatedMar 25, 2025 -
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milopy Public
Python implementation of Milo for differential abundance testing on KNN graph
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cNMF Public
Forked from dylkot/cNMFCode and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
Jupyter Notebook MIT License UpdatedJan 29, 2025 -
pertpy Public
Forked from scverse/pertpyPerturbation Analysis in the scverse ecosystem.
Python MIT License UpdatedJan 3, 2025 -
pertpy-reproducibility Public
Forked from theislab/pertpy-reproducibilityJupyter Notebook Apache License 2.0 UpdatedNov 20, 2024 -
scanpy Public
Forked from scverse/scanpySingle-cell analysis in Python. Scales to >1M cells.
Python BSD 3-Clause "New" or "Revised" License UpdatedOct 23, 2024 -
sc_target_evidence Public
Meta-analysis of drug target evidence in single-cell data
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paperpile2remarkable Public
Script to automate reading and annotating papers from Paperpile library on ReMarkable tablet
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bioframe Public
Forked from open2c/bioframePandas utilities for tab-delimited and other genomic data files
Python MIT License UpdatedApr 7, 2024 -
scverse-tutorials Public
Forked from scverse/scverse-tutorialsTutorials for learning scverse
BSD 3-Clause "New" or "Revised" License UpdatedJan 17, 2023 -
multisample-sc-analysis Public
An overview of datasets and tools for multi-condition single-cell analysis
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pertpy-tutorials Public
Forked from scverse/pertpy-tutorialsJupyter Notebook Apache License 2.0 UpdatedNov 3, 2022 -
cookiecutter-scverse Public
Forked from scverse/cookiecutter-scverseCookiecutter template for scverse
Python BSD 3-Clause "New" or "Revised" License UpdatedOct 31, 2022 -
momicsTools Public
A collection of resources and knowledge for analysis of scATAC+scRNA multi omics data
10 UpdatedSep 16, 2022 -
ncem Public
Forked from theislab/ncemLearning cell communication from spatial graphs of cells
Python BSD 3-Clause "New" or "Revised" License UpdatedAug 12, 2022 -
Materials for EBI Systems Biology course
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sfaira-data-curator Public
Scripts to curate local data stored in h5ad format
Python UpdatedJun 15, 2022 -
starters Public
Forked from Teichlab/startersComputational setup checklist for new starters
1 UpdatedOct 14, 2021 -
pypictionary Public
Interactive python notebook to play pictionary
Jupyter Notebook UpdatedOct 8, 2021 -
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SingleCellOpenProblems Public
Forked from openproblems-bio/openproblemsFormalizing and benchmarking open problems in single-cell genomics
Jupyter Notebook MIT License UpdatedMar 31, 2021 -
scATAC_prep Public
A not-too-orderly collection of scripts for preprocessing and dimensionality reduction of scATAC-seq data
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kbroman.github.io Public
Forked from kbroman/kbroman.github.ioKarl Broman's website
HTML Other UpdatedDec 22, 2020 -
cellatac Public
Forked from cellgeni/cellatacSanger Cellular Genetics single-cell ATAC-seq pipeline.
Nextflow GNU General Public License v3.0 UpdatedMar 27, 2020 -
trajectorama Public
Forked from brianhie/trajectoramaMulti-study integration of cellular trajectories
Python MIT License UpdatedFeb 27, 2020