A complete guide for analyzing bulk RNA-seq data. Go from raw FASTQ files to mapping reads using STAR and differential gene expression analysis using DESeq2, using example data from Guo et al. 2019.
☆127Aug 21, 2020Updated 5 years ago
Alternatives and similar repositories for bulk-rnaseq-analysis
Users that are interested in bulk-rnaseq-analysis are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A guide for analyzing single-cell RNA-seq data using the R package Seurat. Go from raw data to cell clustering, identifying cell types, c…☆29Feb 19, 2020Updated 6 years ago
- Step-by-step analysis pipeline for RNA-seq data☆173Sep 5, 2023Updated 2 years ago
- RNA seq analysis using Bioconductor (analysis built on limma, edgeR)☆12Sep 23, 2022Updated 3 years ago
- scRNA analysis of public dataset on bladder cancer☆20Dec 12, 2025Updated 6 months ago
- Chromatin ACcessibility and Transcriptomics Unifying Software☆18Oct 25, 2024Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Batch Correction and Adaptive Contrast Calling in Complex RNA-seq Experimental Designs Using DESeq2☆17Feb 12, 2026Updated 4 months ago
- ☆43Oct 16, 2024Updated last year
- ☆29Mar 24, 2026Updated 3 months ago
- ☆14Aug 31, 2016Updated 9 years ago
- Scripts used for the Differential NicheNet analyses in the Liver Atlas paper Guilliams et al., Cell 2022☆10Jan 12, 2022Updated 4 years ago
- Visualize cancer genomes with FAIR single-cell RNA-seq data☆13Jan 5, 2023Updated 3 years ago
- ☆25Feb 6, 2025Updated last year
- scripts and notebooks from sanbomics☆471Nov 25, 2024Updated last year
- ☆17Sep 28, 2022Updated 3 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- ☆28Jan 25, 2022Updated 4 years ago
- ☆19Mar 8, 2023Updated 3 years ago
- Brings SingleCellExperiment objects to the tidyverse☆37Nov 10, 2025Updated 7 months ago
- A package that performs cell type annotations on single cell resolution of spatial transcriptomics data, find the niche interactions and …☆16Dec 5, 2025Updated 7 months ago
- RNAseq analysis notes from Ming Tang☆1,090Nov 15, 2021Updated 4 years ago
- ☆21Sep 8, 2023Updated 2 years ago
- ☆10Dec 11, 2024Updated last year
- Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files, rename fasta files (prefix a…☆23Oct 21, 2025Updated 8 months ago
- Physalia course Machine Learning for Multi-Omics Integration☆21Jun 11, 2025Updated last year
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Toolkit for single-cell analysis of chromatin accessibility☆13Feb 27, 2020Updated 6 years ago
- Introduction to bulk RNA-seq☆147Mar 16, 2026Updated 3 months ago
- Code for the manuscript "Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial c…☆25Jun 21, 2022Updated 4 years ago
- BulkSignalR☆27Jun 23, 2026Updated 2 weeks ago
- GCEN: an easy-to-use toolkit for Gene Co-Expression Network analysis and lncRNAs annotation☆22Mar 26, 2022Updated 4 years ago
- A tool for diagnosing SMA in exome, genome or targeted sequencing data☆13Updated this week
- Tutorial for scRNA-seq data analysis beginners using R☆269Mar 5, 2025Updated last year
- https://www.sc-best-practices.org☆1,222Jun 23, 2026Updated 2 weeks ago
- Workflow for single-cell RNA-seq analysis using Seurat☆52Jan 14, 2024Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Scripts and files for the annual Short Read Analysis Workshop☆14Updated this week
- omics data analysis using clusterProfiler ;)☆15Jun 6, 2024Updated 2 years ago
- Code used for mouse single cell RNAseq testis atlas☆12Nov 28, 2020Updated 5 years ago
- Msuite2: integrated DNA methylation data analysis toolkit with enhanced performance☆10Jan 21, 2025Updated last year
- Cookiecutter profile for making a NextFlow-based bioinformatics tool☆17Jul 8, 2024Updated last year
- A growing collection of bioinformatics tutorials, project guides, tools, and articles I’ve developed to make bioinformatics more accessib…☆507Dec 26, 2025Updated 6 months ago
- Conveniently perform ASCAT copy-number analysis from Tumor-Normal or Tumor only BAM files in R☆12Dec 6, 2021Updated 4 years ago