https://github.com/uc-bd2k/GREIN

GREIN : GEO RNA-seq Experiments Interactive Navigator

bioinformatics-analysis bioinformatics-pipeline gene-expression gene-expression-omnibus geo geo-data-processing graphical-interface grein interactive-analysis interactive-visualizations processing r rna-seq rna-seq-analysis rna-seq-data rna-seq-pipeline shiny-apps

Last synced: 06 May 2025

https://github.com/jumphone/sprint

SNP-free RNA editing Identification Toolkit

rna-editing rna-seq rna-seq-analysis rna-seq-mapping rna-seq-pipeline

Last synced: 14 May 2025

https://github.com/czheluo/teach-bioinformatics-r-dataviz

Materials for "Teaching Bioinformatics and R for dataviz course" June-August 2019 in Majorbio

dataviz rna-seq-pipeline teaching-bioinformatics teaching-statistics

Last synced: 13 May 2025

https://github.com/lieberinstitute/speaqeasy

SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.

hisat2 nextflow pipeline rna-seq-pipeline rnaseq rstats speaqeasy

Last synced: 23 Mar 2025

https://github.com/pentalpha/r-peridot

Software for intuitively doing Differential Gene Expression (DGE) analysis on Windows and GNU\Linux, based on R packages.

bioconductor bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-tool differential-expression differential-expression-analysis gene-expression rna-seq-analysis rna-seq-pipeline

Last synced: 05 May 2025

https://github.com/epigen/rnaseq_pipeline

RNA-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

bash bioinformatics biomedical-data-science ngs pipeline python rna-seq rna-seq-pipeline rnaseq snakemake workflow

Last synced: 06 Apr 2025

https://github.com/lioscro/alaska-parse

Automated and friendly RNA-seq analysis (migrated to Parse Server)

automation docker docker-compose kallisto parse-server pipeline python3 rna-seq rna-seq-analysis rna-seq-pipeline rna-sequencing sleuth

Last synced: 05 Apr 2025

https://github.com/sivkri/mirnaseq-de-analysis-qc

Performing RNA-Seq data analysis and quality control using DESeq2 in R.

deseq2 deseq2-analysis differential-expression-analysis quality-control rna-seq rna-seq-analysis rna-seq-data rna-seq-pipeline visualization

Last synced: 22 Mar 2025

https://github.com/angai4/fyp

RNA-seq pipeline automation scripts

perl-script rna-seq-pipeline shell-script

Last synced: 05 Apr 2025

https://github.com/markonyango/quasi-express

bioinformatics deseq2 differential-expression edger gui-application rna-seq rna-seq-pipeline

Last synced: 24 Mar 2025

https://github.com/meeranhussain/rnaseq_degseq_snakemake_no-replicates

Workflow for differential gene expression analysis for non-replicate samples using DEGseq

differential-gene-expression rna-seq-analysis rna-seq-pipeline snakemake-workflow star-aligner

Last synced: 25 Feb 2025

https://github.com/meeranhussain/rnaseq_deseq2_snakemake

Differential gene expression analysis for samples with replicates using STAR-DeSeq2 pipeline

deseq2-analysis differential-gene-expression rna rna-seq-analysis rna-seq-pipeline snakemake-workflow star-aligner

Last synced: 25 Feb 2025

https://github.com/dgrfs/nfcore_rnaseq_cardiff_university_hawk

RNA Sequencing pipeline on Cardiff University Hawk using NF-Core with example data.

nextflow nf-core rna-seq-pipeline

Last synced: 25 Feb 2025

https://github.com/biomystery/rna-seq-snakemake-pipeline

A snakemake RNAseq pipeline using kalisto. Adapted from https://github.com/crazyhottommy/RNA-seq-analysis/tree/master/RNA-seq-snakemake-pipeline

rna-seq-pipeline snakemake

Last synced: 04 Mar 2025

https://github.com/acastanza/seqformat

RNA-seq Preprocessing for GSEA

gsea msigdb rna-seq rna-seq-analysis rna-seq-pipeline

Last synced: 24 Apr 2025

https://github.com/dohlee/snakemake-kallisto-sleuth

Kallisto-sleuth pipeline in snakemake.

bioinformatics bioinformatics-pipeline pipeline rna-seq rna-seq-analysis rna-seq-pipeline

Last synced: 27 Feb 2025

https://github.com/arkanivasarkar/rnaseq-data-analysis-pipeline

Pipeline for analyzing RNAseq data of human and mouse - beginner friendly with minimal user inputs

bioinformatics differential-gene-expression rna-seq rna-seq-pipeline

Last synced: 27 Mar 2025

https://github.com/ssl-bio/degradome-analysis

Pipeline for the analysis of degradome sequencing data using the third party PyDegradome (https://github.com/mgaglia81/PyDegradome) script followed by a custom classification. The pipeline requires a custom R package (https://github.com/ssl-bio/R_postpydeg)

rna-seq-pipeline

Last synced: 23 Mar 2025