Chris Fields's repositories
Bio-Tools-Primer3Redux
A reimplementation of BioPerl's Primer3-related code for primer3 v1 and v2
microbiome_helper
An assortment of scripts to help process and automate various microbiome and metagenomic bioinformatic tools.
NGI-RNAseq
Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
p6-Bio-HTSLib
Perl6 NativeCall bindings to htslib
Bio-Root-MOP
Moose-based Bio::Root bridge classes (testing for BioPerl)
common-workflow-language
Repository for CWL Specifications. Use https://www.biostars.org/t/cwl/ for support.
datasciencecoursera
Temp repo for Data Science Toolbox course
genomediff-python
GenomeDiff (*.gd) file parser for Python
github-paper
Plos in Computational Biology paper related with github for researchers, code, source and document
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
redmine2github
Scripts to migrate redmine tickets to github issues
bosc-review-of-reviews
This repository contains scripts for collating abstract reviews from EasyChair
bosc_materials
Misc. documents for the Bioinformatics Open Source Conference (BOSC), https://www.open-bio.org/events/bosc/
H3ABionet-SOPs
Standard operating procedures for H3ABionet data processing and analyses
obf-docs
Official documents of the Open Bioinformatics Foundation
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:
samblaster
samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
sig-bio-shiny
A standalone R shiny application for doing significant biology on a set of genes
test-actions
Short-lived repo to test actions