A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
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Jan 21, 2025 - Python
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differential-expression
Here are 181 public repositories matching this topic...
Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
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Jun 4, 2024 - HTML
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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May 30, 2023 - Python
Brings bulk and pseudobulk transcriptomics to the tidyverse
pipe tidy-data tidyverse pca bioconductor deseq2 entrez tidy transcripts transcriptomics tsne differential-expression edger redundancy gsea tibble gene-symbols bulk-transcriptional-analyses mds-dimensions ensembl-ids
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Jan 19, 2025 - R
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
systems-biology scrna-seq single-cell differential-expression single-cell-rna-seq intercellular-communication ligand-receptor ligand-target cell-cell-interaction cell-cell-communication ligand-receptor-interaction intercellular-signaling
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Jan 14, 2025 - HTML
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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Jan 20, 2025 - Python
integrated RNA-seq Analysis Pipeline
rna-seq pipeline gene-expression rna-seq-analysis differential-expression transcript-quantification single-cell-rna-seq irap bulk-rna-seq exon-quantification
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Feb 6, 2019 - R
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
workflow rna-seq pipeline nextflow shiny deseq2 microarray chip-seq atac-seq differential-expression limma gsea nf-core differential-abundance
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Jan 22, 2025 - Nextflow
Porting DESeq2 into python via rpy2
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Jun 1, 2023 - Python
R package for pathway analysis in scRNA-seq data
r-package transcriptomics single-cell pathway-analysis differential-expression single-cell-rna-seq gene-signatures
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Aug 17, 2024 - R
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
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Jan 26, 2025 - Python
Compare different differential abundance and expression methods
metagenomics rnaseq auc proteomics metabolomics microbiome false-positive-control differential-expression 16s otu marker-gene-analysis relative-abundances compare-methods differential-abundance-methods
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Mar 8, 2022 - R
Explore and share your scRNAseq clustering results
r ui shiny scrna-seq single-cell differential-expression clustering-evaluation scrnaseq scrna-seq-analysis
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Sep 6, 2023 - R
Experimental design framework for scRNAseq population studies (eQTL and DE)
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Jan 8, 2025 - R
Best practice RNA-Seq analysis pipeline for reference-based RNA-Seq analysis
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May 17, 2021 - Shell
An R package to plot interactive three-way differential expression analysis
package cran bioinformatics rna-seq interactive plotly gene-expression omics transcriptomics differential-expression differential-expression-analysis volcanoplots
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Aug 25, 2023 - HTML
UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets
workflow pipeline nextflow rna transcriptome rna-seq-analysis differential-expression lncrna non-coding nf-core long-non-coding
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May 9, 2024 - Nextflow
Interactive Differential Expression AnaLysis - DE made accessible and reproducible
rna-seq r shiny reproducible-research bioconductor user-friendly rna-seq-analysis differential-expression
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Dec 19, 2024 - R
pseudobulking on an AnnData object
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Jun 30, 2023 - Python
Differential analysis of multi-omics data based on the Tweedie distribution
metagenomics microbiome single-cell differential-expression multi-omics-data differential-abundance-analysis
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Aug 8, 2024 - R
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