Mark Diekhans

Login: diekhans

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Repositories

bd2k-python-lib

The BD2K Python module kitchen sink

cactus

Genome aligner based upon notion of Cactus graphs

cgtBuild

Vuild of Cactus and Compatative Genomics Toolkit, including dependencies

chunkyMonkey

Completely useless toy for experimenting with chunked encoding

Comparative-Annotation-Toolkit

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cPecan

C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.

cpython

The Python programming language

eutils

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

ga4gh-compliance

A compliance test suite for the APIs defined in the schemas repository.

ga4gh-schemas

Work on data models and APIs for Genomic data.

ga4gh-server

A reference implementation of the APIs defined in the schemas repository.

gencode-backmap

Mapping of GENCODE gene annotation set files to older assembies

gencode-icedb

GENCODE Independently Collected Evidence Database

hal

Hierarchical Alignment Format

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

intronProspector

Identify putative introns in RNA-Seq alignments

lastz-dist

Import of lastz distribution

luigi

Luigi is a Python module that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization etc. It also comes with Hadoop support built in.

matchingAndOrdering

Library of matching and ordering algorithms, used for the "reference problem"

nanopore-track-hub

Track hubs for https://github.com/nanopore-wgs-consortium/

ontobio

python library for working with ontologies and ontology associations

pinchesAndCacti

Library for constructing pinch graphs and cactus graphs

pipettor

robust, easy to use Python package for running Unix process pipelines

prefixcommons-py

Prefix commons python utlities

progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules

pubMunch

various tools to download, convert and process the full text of scientific articles

pycbio

pycbio

pytabix

:card_index: Retrieve data in genomic intervals with a Python interface for tabix.

repo-play

Experiment with repo and GA4GH

sonLib

Small general-purpose library for C and Python with an emphasis on bioinformatics.

sphinx

Main repository for the Sphinx documentation builder

synteny-play-ground

some experimentation

tebreak

Find and characterise transposable element insertions

toil

Toil is a scalable, efficient, cross-platform pipeline management system, written entirely in Python, and designed around the principles of functional programming.

twobitreader

A fast python class for reading 2-bit files (used by UCSC genome browser)

UCSC-GENCODE-2018

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Commits To