gpratt

gatk

GATK Official Release Repository

iPython_Notebook

adaptivebiotech_exercise

Programming Exercise for Adaptive Biotech

aizawa

Analysis Scripts For Aizawa Lab

clipper

A tool to identify CLIP-seq peaks

dagr

A scala based DSL and framework for writing and executing bioinformatics pipelines as Directed Acyclic GRaphs

fgbio

Tools for working with genomic and high throughput sequencing data.

gatk_queue_tutorial

gffutils

GFF and GTF file manipulation and interconversion

gpratt.github.io

Personal Blog

gscripts

General Use Scripts and Helper functions

htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

nbviewer

Nbconvert as a webservice (rendering ipynb to static HTML)

PIPE-CLIP

processing_scripts

scripts for processing data

pybedtools

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

Ren_Rotation

Code for Ren Lab Rotation

sampleproject

A sample project that exists for PyPUG's "Tutorial on Packaging and Distributing Projects"

screed

a simple read-only sequence database, designed for short reads

shovill

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

trackhub

create, manage, and upload track hubs for use in the UCSC genome browser

tscc_ipython

ucsd-thesis

UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets