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deseq2
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RNA-seq workflow using STAR and DESeq2
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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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Statistical Analysis of RNA-Seq Tools
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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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- Nextflow
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R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/
count gene r human rstats bioconductor rnaseq deseq2 illumina exon junction derfinder annotation-agnostic recount
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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
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Differential gene expression analysis and pathway analysis of RNAseq data
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NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization
docker bioinformatics rna-seq web-application deseq2 shiny-apps single-cell bioinformatics-analysis seurat nasqar
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TUCCA's RNA-Seq Workflow for Read Quantification, Differential Expression, and Pathway Enrichment Analysis
bioinformatics quality-control rna-seq snakemake conda singularity deseq2 ideal reproducibility high-throughput transcriptomics salmon differential-expression snakemake-workflow pathway-enrichment-analysis renv clusterprofiler apptainer genetonic pcaexplorer
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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
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A quick recap of widely used differential analyses methods in R for RNA-seq experiments
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Differential expression analysis: DESeq2, edgeR, limma. Realized in python based on rpy2
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a web-based R shiny application that wraps DESeq2 R package
visualization bioinformatics rna-seq r shiny rshiny deseq2 rna-seq-analysis shinyapps webapplication bulk-rna-seq
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- R
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