This repository has snakemake scripts for salmon-deseq2 pipeline for RNAseq data analysis
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Jun 7, 2018 - R
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salmon-deseq2
Here are 8 public repositories matching this topic...
Performed a differential gene expression analysis with RNA-seq that compares the expression in human control breast cancer cell lines with lines treated by silencing the NRDE2 gene. A Salmon + tximport + DESeq2 workflow was conducted to pursue this.
linux unix bioinformatics rna-seq r hpc rstudio ngs next-generation-sequencing bioinformatics-pipeline rnaseq deseq2 rna-sequencing salmon rna-seq-analysis rna-seq-data ngs-analysis rna-seq-pipeline salmon-deseq2 tximport
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Aug 28, 2020 - Shell
This repo contains code to pre-process, quant, and analyze RNA-Seq data obtained from human enteriod cell cultures
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Dec 28, 2022 - Shell
Jupyter notebooks for DGE results and ontology analysis and visualisation.
data-visualization deseq2 transcriptomics salmon dge salmon-deseq2 deseq2-analysis ontology-analysis
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Feb 28, 2025 - Jupyter Notebook
Simple Nextflow RNA-Seq pipeline
rna-seq r nextflow bioconductor deseq2 salmon rna-seq-analysis miniconda miniconda-environments miniconda3 rna-seq-pipeline dge-analysis salmon-deseq2 nextflow-pipeline nextflow-rnaseq
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Jan 24, 2024 - Nextflow
Simple Snakemake RNA-Seq pipeline
python rna-seq snakemake r pandas python3 bioconductor salmon miniconda dge miniconda3 dge-analysis salmon-deseq2 rnaseq-pipeline snakemake-pipeline rnaseq-analysis snakemake-rna-seq
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Mar 21, 2023 - Python
Repository for bulk RNA-seq analyses (from undergrad 2nd-3rd year) – Reorganized
hisat2 salmon bioconductor-packages samtools edger limma cran-r fastqc rna-seq-pipeline bulk-rna-seq salmon-deseq2 sra-toolkit feature-counts deseq2-pipeline
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Oct 20, 2025 - R
`rnaseq_pipeline` is a reproducible, end-to-end bulk RNA-seq workflow that takes you from raw FASTQ files to publication-ready results
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Dec 21, 2025 - Shell
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