A collection of IPython notebooks covering various topics.

📚 Freely available programming books

Summer school course materials collection

Tools to process and analyze deep sequencing data.

ENCODE ATAC-seq pipeline

SRA Tools

ATAC-seq Quality Control

Merging paired-end reads and removing adapters

Jupyter metapackage for installation, docs and chat

Documentation and Developers Code Base for Iso-Seq SMRTAnalysis 3.x and beyond

🎓 A collection of interactive courses for the swirl R package.

An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study

ATAC-seq and DNase-seq processing pipeline

Bioinformatics one liners from Ming Tang

The repository keeps the files for an IPython notebook on about how to make a simple genome assembler using python

Bioconductor package: An Easy-to-use Systematic pipeline for ATACseq data analysis

Tools for processing and analyzing pooled Genetic Interaction map data

Applied Computational Genomics Course at UU: Spring 2018

http://tinyurl.com/cruk-stats

Introduction to Statistics using Python

nucleosome calling using ATAC-seq

STAR based ENCODE Long RNA-Seq processing pipeline

An Introduction to Statistical Learning (James, Witten, Hastie, Tibshirani, 2013): Python code

ph525x. functions only, no data

Rmd source files for the HarvardX series PH525x

Compiled and pretty version of labs

Random utility scripts for genomics data

A Course on designing high-throughput experiments

A online presentation for sed & awk