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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

GATK Official Release Repository

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.

ipython_notebook

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