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Mark Diekhans (diekhans)

diekhans

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Company:UCSC

Location:Santa Cruz, CA, US

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Mark Diekhans's repositories

gencode-backmap

Mapping of GENCODE gene annotation set files to older assembies

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intronProspector

Identify putative introns in RNA-Seq alignments

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pycbio

pycbio

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pipettor

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

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PrimerS-JuJu

Tools to assist with primer design

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t2t-chm13-gene-analysis

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isoseq-xspecies

ISO-Seq crosss-species analysis

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awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

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bioconda-recipes

Conda recipes for the bioconda channel.

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cactus

Genome aligner based upon notion of Cactus graphs

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duplicacy

A new generation cloud backup tool

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flair

Full-Length Alternative Isoform analysis of RNA

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HPRC_Assembly_Hub

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htslib

C library for high-throughput sequencing data formats

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kent

UCSC Genome Browser source tree. Stable branch: "beta".

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Liftoff

An accurate GFF3/GTF lift over pipeline

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lrgasp-experimental-eval

lrgasp-experimental-eval

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LyRic

Long RNA-seq analysis workflow

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miniprot

Align proteins to genomes with splicing and frameshift

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paffy

Small C/CLI library of paf format tools used by Cactus

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play

just experimenting

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pyexiftool

PyExifTool (active PyPI project) - A Python library to communicate with an instance of Phil Harvey's ExifTool command-line application. Runs one process with special -stay_open flag, and pipes data to/from. Much more efficient than running a subprocess for each command!

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pyexiftool-bug

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SQANTI3

Tool for the Quality Control of Long-Read Defined Transcriptomes

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sqantiTools

Various tools to work with data from SQUANTI3

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T2T-CHM13-hub

Assembly hub for T2T CHRM13 assemblies

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t2t-primates-hub

Hub for the T2T Primates Project

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taffy

This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files

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transcript-frame-tools

Various toos to validate exon frames and CDS in gene annotation (not generally useful)

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transMap

TransMap pipeline used to build cross-species tracks for UCSC browser

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