Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data

Estimation of Promoter Activity from RNA-Seq data

GREIN : GEO RNA-seq Experiments Interactive Navigator

Interactive R package to quantify, analyse and visualise alternative splicing

🔬 A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data

Exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.

The code and analyses accompanying the manuscript “MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data”.

RNAdetector: a free user-friendly and stand-alone software for RNA-Seq data analysis

🌻 View single-cell RNA-seq and mass cytometry data in synovial tissues from patients with RA or OA.

M5NRv2 -- non-redundant protein and rRNA database integration

Epigenomics workflow system for the semi-automated analysis of NGS data

Collection of scripts to map eQTL with RNAseq Data and Genotype by Sequencing

DEWE (Differential Expression Workflow Executor) is an open source application for easily executing Differential Expression analyses in RNA-Seq data.

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.