Tools for working with SAM/BAM data

A fast and sensitive gapped read aligner

By study this, it won't be costly or time-consuming to customize a NGS data analysis pipeline

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

A library for transfer learning by reusing parts of TensorFlow models.

Google Brain AutoML

The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.

HMS Research Computing User Training

RNAseq analysis notes from Ming Tang

Copy number calling and variant classification using targeted short read sequencing

JAMM Peak Finder for Sequencing Datasets

ChIP-seq analysis notes from Ming Tang

A quality control analysis tool for high throughput sequencing data

Python biomart API

Genomic Data Retrieval with R

HMMRATAC peak caller for ATAC-seq data

Command-line tool for the visualization of splicing events across multiple samples

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

Cutadapt removes adapter sequences from sequencing reads

The Python programming language

RNA-seq workflow: differential transcript usage

June 5, 2019

Open source Markdown editor for macOS.

Statistical Analysis of RNA-Seq Tools

Documentation of the Snakemake-Workflows project

iCellR is an interactive R package designed to facilitate the analysis and visualization of high-throughput single-cell sequencing data. It supports a variety of single-cell technologies, including…

Tutorials on accessing public reference and genomic data