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awesome-single-cell

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

awesome-wsl

Awesome list dedicated to Windows Subsystem for Linux

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

in-depth-ngs-data-analysis-course

Materials for 12-day course on analyzing RNA-Seq, ChIP-Seq and variant calling data.

kallisto

Near-optimal RNA-Seq quantification

kimlab

rna-seq-analysis

RNAseq analysis notes from Ming Tang

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

rsem

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments

sartools

Statistical Analysis of RNA-Seq Tools

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

sleuth

Differential analysis of RNA-Seq

stringtie

Transcript assembly and quantification for RNA-Seq

tximport

Import and summarize transcript-level estimates for gene-level analysis