Andrew Warren's repositories
sra_import_orig
SRA import for PATRIC
TrimGalore
A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
gffutils
GFF and GTF file manipulation and interconversion
p3_docs
This repository is for manage PATRIC static contents such as Website Tutorial, CLI Tutorial, User Guides, and PATRIC eNews.
GOGranny
A python library for representing and using the Gene Ontology
stringtie
Transcript assembly and quantification for RNA-Seq
go-site
A collection of metadata, tools, and files associated with the Gene Ontology public web presence.
goatools
Python scripts to find enrichment of GO terms
pangenome_layout
Layout pangenome graphs using gephi toolkit
gexf-js
A JavaScript GEXF viewer
pg-graph-server
Web server for creating pan-genome graphs
p3_trees-1
to implement deployment structures around newly generated trees for display on the site
msa
Modular BioJS compoment for a multiple sequence alignment
p3api
p3api dev
msa-tree
A modular combination of MSA viewer and phylogenetic tree viewer
Rockhopper
For computational analysis of bacterial RNA-seq data
setup-scripts
scripts for custom build enviorments
patric_solr_export
Temporary export of solr schema for sharing. WARNING: could be out of date
msa-test
Simple html page for testing side by side msa tree. Needs biojs: msa, msa-tnt, and biojs-io-newick
wasabi-app
Automatically exported from code.google.com/p/wasabi-app
wasabi-patric
wasabi msa viewer
pangenome_examples
GEXF example files of pan-genome graphs
GTF-to-Operon
Combines existing annotation with GTF Transcript assembly by Cufflinks.
gexfd3
A small library for rendering parsed GEXF graphs in D3.js
biopython
Official git repository for Biopython (converted from CVS)
jbrowse
A modern genome browser built with JavaScript and HTML5.