Pinned Repositories
Bio-Kseq
Perl XS bindings to klib's kseq.h
Bio-Parse
Low level biological data parsers
Bio-Stream
Generic streams for BioPerl parsing
Bio-Tools-Primer3Redux
A reimplementation of BioPerl's Primer3-related code for primer3 v1 and v2
bio.brew
A tiny package manager for crucial unix and bioinformatics tools
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
bioperl6
reimplementation of BioPerl classes in Raku (e.g. the language formerly known as Perl6)
pBWA
Parallel bwa implementation
readfq
Fast multi-line FASTA/Q reader in several programming languages
cjfields's Repositories
cjfields/bioperl6
reimplementation of BioPerl classes in Raku (e.g. the language formerly known as Perl6)
cjfields/biome
An experimental Moose-based BioPerl implementation
cjfields/Bio-Tools-Primer3Redux
A reimplementation of BioPerl's Primer3-related code for primer3 v1 and v2
cjfields/microbiome_helper
An assortment of scripts to help process and automate various microbiome and metagenomic bioinformatic tools.
cjfields/NGI-RNAseq
Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
cjfields/p6-Bio-HTSLib
Perl6 NativeCall bindings to htslib
cjfields/Bandage
a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
cjfields/Bio-HTS
Source for the CPAN Bio::DB::HTS module. Perl adaptors into the HTSlib library.
cjfields/Bio-Root-MOP
Moose-based Bio::Root bridge classes (testing for BioPerl)
cjfields/bold
Interface to the Bold Systems barcode webservice
cjfields/bp6-bug
Lexical loading bug?
cjfields/common-workflow-language
Repository for CWL Specifications. Use https://www.biostars.org/t/cwl/ for support.
cjfields/datasciencecoursera
Temp repo for Data Science Toolbox course
cjfields/genomediff-python
GenomeDiff (*.gd) file parser for Python
cjfields/github-paper
Plos in Computational Biology paper related with github for researchers, code, source and document
cjfields/p6-Bio-Samtools
Perl6 binding to samtools
cjfields/p6-Crypt-Bcrypt
Bcrypt password hashing in Perl6
cjfields/p6-File-Temp
Simple implementation of File::Temp for creating temporary files
cjfields/panda
Perl 6 module management solution, -Ofun
cjfields/redmine2github
Scripts to migrate redmine tickets to github issues
cjfields/bosc-review-of-reviews
This repository contains scripts for collating abstract reviews from EasyChair
cjfields/bosc_materials
Misc. documents for the Bioinformatics Open Source Conference (BOSC), https://www.open-bio.org/events/bosc/
cjfields/H3ABionet-SOPs
Standard operating procedures for H3ABionet data processing and analyses
cjfields/HPCBio-Refgraph_pipeline
cjfields/obf-docs
Official documents of the Open Bioinformatics Foundation
cjfields/phyloseq
phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
cjfields/planets
cjfields/samblaster
samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
cjfields/sig-bio-shiny
A standalone R shiny application for doing significant biology on a set of genes
cjfields/test-actions
Short-lived repo to test actions