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tidybulk

tidyomics /tidybulk

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

UpdatedNov 12, 2025
R

PF2-pasteur-fr /SARTools

Statistical Analysis of RNA-Seq Tools

rna-seq r reproducible-research deseq2 edger differential-analysis

UpdatedOct 9, 2025
R

amarinderthind /RNA-seq-tutorial-for-gene-differential-expression-analysis

This RNAseq data analysis tutorial is created for educational purpose

tutorial rna-seq r analysis ngs gene-expression pca-analysis rnaseq deseq2 bioconductor-packages enrichment-analysis edger ngs-analysis rnaseq-workshop reactome-pathway rnaseq-pipeline rna-seq-dge

UpdatedFeb 18, 2026
R

eonurk /RNA-seq-differential-analyses-guideline

A quick recap of widely used differential analyses methods in R for RNA-seq experiments

deseq2 edger limma rna-seq-pipeline limma-voom limma-trend

UpdatedDec 7, 2024

peterlipan /DE_rpy2

Differential expression analysis: DESeq2, edgeR, limma. Realized in python based on rpy2

pandas deseq2 differential-expression edger limma rlanguage deseq2-analysis

UpdatedMay 7, 2021
Jupyter Notebook

AyehBlk /RAPTOR

RNA-seq Analysis Pipeline Testing and Optimization Resource - Intelligent pipeline selection and comprehensive benchmarking.

python benchmarking machine-learning rna-seq genomics deseq2 transcriptomics salmon kallisto featurecounts edger rna-seq-pipeline bulk-rna-seq differential-expression-analysis streamlit limma-voom pipeline-benchmarking pipeline-comparison

UpdatedFeb 20, 2026
Python

leekgroup /regionReport

Generate HTML report for a set of genomic regions or DESeq2/edgeR results

r rmarkdown rstats bioconductor rnaseq deseq2 derfinder edger regionreport

UpdatedJan 14, 2025
R

charles-plessy /tutorial

Various tutorials on how to analyse transcriptomic data.

tutorial transcriptome edger cage fantom

UpdatedJun 28, 2023
HTML

stemangiola /ppcseq

Probabilistic outlier identification for bulk RNA sequencing data

r rnaseq deseq2 bayesian-inference stan edger outlier negative-binomial

UpdatedJan 19, 2024
R

EmoryIntegratedComputationalCore /Methods

Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.

rna-seq notebook bioconductor deseq2 methods rna-seq-analysis edger omics-experiments ldm microbiome-analysis phyloseq rna-seq-pipeline emory qiime2 bayseq qvalue discovery-rates comparison-groups analytical-processes

UpdatedMar 21, 2023
R

jahnavigbedre /differentialexpressionanalysis

Differential expression analysis of miRNAs using edgeR and validated target retrieval with multiMiR.

bioinformatics rna-seq ngs gene-expression rstats transcriptomics differential-expression edger mirna target-prediction multimir

UpdatedSep 9, 2025
R

jessmhoehner /Methods

Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.

r metagenomics rnaseq deseq2 metabolomics 16s proteus edger ldm microbiome-analysis phyloseq transcriptomics-data proteomics-data-analysis bayseq qvalue

UpdatedNov 2, 2020
R

Soullevram /Transcriptomics-Analysis-of-Human-Lung-Fibroblast

A R-based analysis of the effect of Cystic Fibrosis on the lung fibroblast transcriptome in humans.

transcriptomics differential-expression edger limma-voom cystic-fibrosis

UpdatedJun 18, 2025
HTML

hernanmd /edgeR.EnhancedVolcanoPlot

Enhanced volcano plot using edgeR data

bioinformatics rna-seq r rnaseq edger volcano

UpdatedJun 26, 2018
R

shussin245 /RNA-Seq-Analysis

This project provides a reproducible workflow for bulk RNA-Seq data analysis, including preprocessing, quality control, differential expression analysis, and visualization using edgeR and limma-voom. It focuses on evaluating pipeline performance while analyzing RNA-Seq data from a case study on mouse mammary gland gene expression.

rna-seq-analysis edger differential-expression-analysis limma-voom

UpdatedDec 30, 2024
HTML

hshim1 /Bulk-RNAseq-visualization-workflow-ZRN01

🧬Custom Bulk RNA-seq workflow for QC, DESeq2 differential expression, and visualization in R 🧬 (RNA-seq, bioinformatics, bulk-rnaseq, visualization, DESeq2, edgeR)

visualization bioinformatics quality-control rna-seq r rstudio ngs bioinformatics-pipeline deseq2 omics rna-seq-analysis edger differential-gene-expression ngs-analysis omics-analysis rnaseq-pipeline deseq2-pipeline

UpdatedSep 17, 2025
RMarkdown

pwilmart /Sea_lion_urine_SpC

Sea lion urine comparison with spectral counting.

r jupyter-notebook proteomics edger paw-pipeline spectral-counts spectral-counting

UpdatedSep 2, 2019
HTML

PF2-pasteur-fr /SARTools-Galaxy

Galaxy wrappers for SARTools (Statistical Analysis of RNA-Seq Tools)

rna-seq r reproducible-research deseq2 galaxy edger differential-analysis

UpdatedJan 6, 2021
R

snbogan /Sp_RRBS_ATAC

Analyses combining ATAC-seq, RRBS, and RNA-seq data for purple urchins

rna-seq genomics expression epigenetics atac-seq rrbs edger splicing

UpdatedMar 13, 2023
R

aprezvykh /bioinformatics

some scripts to process transcriptomics and Chip-seq data

r rnaseq deseq2 reactome edger gage gsea pathview topgo

UpdatedMay 10, 2019
R

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