A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
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Apr 21, 2025 - Python
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differential-expression
Here are 29 public repositories matching this topic...
Differential expression analysis for single-cell RNA-seq data.
bioinformatics tensorflow transcriptomics gene-set-enrichment differential-expression single-cell-rna-seq
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Feb 25, 2025 - Python
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
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Apr 15, 2025 - Python
Porting DESeq2 into python via rpy2
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Jun 1, 2023 - Python
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
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Apr 24, 2025 - Python
pseudobulking on an AnnData object
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Mar 14, 2025 - Python
Fit generalized linear models in python.
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Mar 6, 2023 - Python
Interactive visualizations for differential expression
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Dec 8, 2022 - Python
A robust model for quantitative comparison of ChIP-Seq data sets.
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May 18, 2020 - Python
Discrete Distributional Differential Expression
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Jan 3, 2019 - Python
Causal inference, differential expression, and co-expression for scRNA-seq
scrna-seq single-cell hypothesis-testing differential-expression causal-inference normalization co-expression gene-regulatory-network single-cell-crispr-screening association-testing
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Nov 4, 2021 - Python
A federated implementation of PyDESeq2, based on Substra.
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Apr 16, 2025 - Python
Curare - A customizable and reproducible analysis pipeline for RNA-Seq experiments
bioinformatics rna-seq pipeline reproducibility transcriptomics differential-expression differential-gene-expression
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Apr 4, 2025 - Python
Provided tool will add explicit 3'UTR and extends it into a valid Ensembl GTF file. It's useful for 3'RNAseq when 3' coordinates might not be as good as you expect.
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Apr 28, 2024 - Python
Differential analysis of targeted Isotope-labeled Metabolomics data
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Sep 23, 2024 - Python
NASA GeneLab Open API
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Oct 3, 2023 - Python
Perform differential analysis from FastQ files with Salmon, tximport, and DESeq2
reproducible-research bioinformatics-pipeline deseq2 salmon differential-expression snakemake-workflows tximport
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Aug 18, 2021 - Python
Testing, development environment for a new project of KN BIBS
bioinformatics gene-expression pathways gene-set-enrichment pathway-analysis differential-expression gsea
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Oct 30, 2018 - Python
Transcriptiome Analysis in Python Imported from R
statistics gene-expression survival-analysis plotting transcriptomics gene-set-enrichment differential-expression
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Aug 23, 2022 - Python
Analysis pipeline for bulk RNA-seq data
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Aug 18, 2022 - Python
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