Chris Fields

Login: cjfields

Company: @HPCBio @NCSA-Open @bioperl

Location: University of Illinois UC

Bio: null

Blog: bioperl.org

Blog: bioperl.org

Member of

1. BioPerl
2. biosql
3. Generic Model Organism Database Project
4. High Performance Biological Computing
5. Open Bioinformatics Foundation

Repositories

ActiveResource

The Perl implementation of ActiveResource

AMPHORA2

An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.

assemblage

Tools for working with second gen assemblies, fasta sequences, etc

bamtools

API and toolkit for reading, writing, and manipulating BAM (genome alignment) files

bcbio.variation

Toolkit to analyze genomic variation data, built on the GATK with Clojure

bedtools

A flexible suite of utilities for genome arithmetic. That is, set theory on genomic features.

bio.brew

A tiny package manager for crucial unix and bioinformatics tools

bio-gff3

fast, low-level GFF3 manipulation in Perl

Bio-HTS

Source for the CPAN Bio::DB::HTS module. Perl adaptors into the HTSlib library.

bioinformatics

Tools for bioinformatics

Bio-Kseq

Perl XS bindings to klib's kseq.h

biolib

BioLib brings together a set of opensource libraries written in C/C++ and makes them available for all Bio* languages

biome

An experimental Moose-based BioPerl implementation

Bio-PacBio

General BioPerl modules for PacBio-related tools (EXPERIMENTAL)

Bio-Parse

Low level biological data parsers

bioperl6

reimplementation of BioPerl classes in Perl6

bioperl-collection

submodule test for bioperl repos

Bio-Root-MOP

Moose-based Bio::Root bridge classes (testing for BioPerl)

Bio-Stream

Generic streams for BioPerl parsing

Bio-Tools-Primer3Redux

A reimplementation of BioPerl's Primer3-related code for primer3 v1 and v2

bp6-bug

Lexical loading bug?

common-workflow-language

Repository for CWL Specifications. Use https://www.biostars.org/t/cwl/ for support.

datasciencecoursera

Temp repo for Data Science Toolbox course

datasharing

The Leek group guide to data sharing

Dist-Zilla-PluginBundle-CJFIELDS

My Dist::Zilla plugin bundle (or bungle, depending on how you look at it)

fastq-tools

Small utilities for working with fastq sequence files.

genomediff-python

GenomeDiff (*.gd) file parser for Python

github-paper

Plos in Computational Biology paper related with github for researchers, code, source and document

issue-migration-test

test bioperl issue migration

khmer

in-memory k-mer counting

NGI-RNAseq

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

p6-Bio-HTSLib

Perl6 NativeCall bindings to htslib

p6-Bio-Samtools

Perl6 binding to samtools

p6-Crypt-Bcrypt

Bcrypt password hashing in Perl6

p6-File-Temp

Simple implementation of File::Temp for creating temporary files

panda

Perl 6 module management solution, -Ofun

pBWA

Parallel bwa implementation

readfq

Fast multi-line FASTA/Q reader in several programming languages

redmine2github

Scripts to migrate redmine tickets to github issues

redmine_github_hook

Allow your Redmine installation to be notified when changes have been pushed to a Github repository.

redmine-issues-to-github

Reads issues from a redmine API XML and adds them to a github repository.

sambamba

Tools for working with SAM/BAM data (development suspended until July)

samtools

null

seqtk

null

SVG-Graph

Visualize Graph.pm data in SVG

Wright

null

Commits To