Clustering scRNAseq by genotypes
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Apr 30, 2026 - Python
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scrna-seq-analysis
Here are 34 public repositories matching this topic...
scGNN (single cell graph neural networks) for single cell clustering and imputation using graph neural networks
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Jul 25, 2024 - Python
Memory-efficient single-cell analysis in Python. Stream RNA, ATAC, CITE-seq and multi-omics from local or remote Zarr stores, from laptop to atlas scale, with reusable fingerprinted results.
single-cell object-storage single-cell-omics scrna-seq-analysis single-cell-multiomics scalable-computing provenance-tracking
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Aug 7, 2026 - Python
Quantifying experimental perturbations at single cell resolution
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Sep 27, 2024 - Python
An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data
scrna-seq single-cell fastq demultiplexing single-cell-rna-seq single-cell-analysis single-cell-omics scrna-seq-analysis single-cell-sequencing split-seq
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Oct 4, 2023 - Python
A permutation-free framework for scalable, robust, and reference-based cell-cell communication analysis in single cell transcriptomics studies
single-cell scrna-seq-analysis cell-cell-communication permutation-free fastccc human-ccc-reference-panel
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May 23, 2026 - Python
Single cell type annotation guided by cell atlases, with freedom to be queer
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Jul 25, 2022 - Python
Perturbational analysis by causality-aware generative model for single-cell RNA-sequencing data
bioinformatics causal-inference treatment-effects batch-effects perturbation-analysis scrna-seq-analysis causal-machine-learning insilico-prediction
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Dec 16, 2025 - Python
Single cell analysis using Low Resource
machine-learning bioinformatics deep-learning neural-network bioinformatics-pipeline single-cell biomarker-discovery scrna-seq-analysis
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Apr 3, 2026 - Python
The simplest repo for scGPT inference, finetuning and training.
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Jul 14, 2026 - Python
Single-cell eQTL mapping and causal gene regulatory network inference at high efficiency and accuracy
causal-inference gene-regulatory-network mendelian-randomization scrna-seq-analysis eqtl-mapping single-cell-multiomics
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Jul 6, 2026 - Python
PHet: Heterogeneity-Preserving Discriminative Feature Selection for Subtype Discovery
single-cell scrna-seq-analysis microarray-data-analysis patient-subtyping cell-types subtype-finding
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Oct 2, 2025 - Python
Folded and map strategy and cell perturbation response prediction
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Dec 14, 2022 - Python
orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.
python bioinformatics evolution gene-expression transcriptome gene-expression-profiles orthofinder tai scrna-seq-analysis phylostratigraphy scanpy expression-profiles orthomap
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Nov 20, 2023 - Python
scSPARKL is an Apache spark based pipeline for performing variety of preprocessing and downstream analysis of scRNA-seq data.
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Aug 8, 2025 - Python
Gardener is an agentic system for single-cell RNA-seq analysis. Its intuitive GUI automates complex workflows, sharpens clustering, and supports deeper biological reasoning. You can easily branch, revert, and compare experiments for full analytical control. All data stays strictly on your local device, ensuring complete privacy and security.
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Jul 31, 2026 - Python
PyPairs - A python scRNA-Seq classifier
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Feb 17, 2021 - Python
This repository houses a workflow that uses biological feature trees to segregate cancer RNA-seq datasets, then it trains machine learning models to predict the presence or absence of known, cancer-associated DNA-level mutations.
machine-learning rna-seq cancer-genomics scrna-seq cancer-research cancer-detection early-detection machinelearning-python scrna-seq-analysis cancer-prediction
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Oct 11, 2023 - Python
The integration tool for 15 single cell RNA velocity algorithms
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Jan 8, 2025 - Python
An effective tool for single-cell RNA sequencing.
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Apr 19, 2024 - Python
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