The Lab for Data Intensive Biology

Previously "Genomics, Evolution, and Development Lab" @ Michigan State University

University of California, Davis, School of Veterinary Medicine, Davis, California, USA

Pinned Repositories

2018-ncbi-lineages
Extract lineage CSVs from NCBI for use with sourmash lca.
Language:Python27 4 06
charcoal
Remove contaminated contigs from genomes using k-mers and taxonomies.
Language:Python53 19 1631
dammit
just annotate it, dammit!
Language:Python89 13 16528
dib-MMETSP
Code to generate re-assemblies of the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP)
Language:Python21 8 36
elvers
(formerly eelpond) an automated RNA-Seq workflow system
Language:Python28 6 993
genome-grist
map Illumina metagenomes to genomes!
Language:Jupyter Notebook37 23 1726
khmer
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
Language:Python757 68 1k295
khmer-protocols
Language:Python19 29 7724
pybbhash
A Python wrapper for the bbhash library for Minimal Perfect Hashing
Language:C++18 6 114
screed
a simple read-only sequence database, designed for short reads
Language:Python64 25 1134

The Lab for Data Intensive Biology's Repositories

dib-lab/2016-pycon-tutorial
Materials for "Creating, building, testing, and documenting a Python project - a hands-on HOWTO - PyCon 2016"
17 18 66
dib-lab/SSUsearch
A pipeline for extracting SSU rRNA gene from wgs data and applying them for further diversity analysis
Language:Jupyter Notebook10 19 01
dib-lab/2012-paper-diginorm
Paper source, analysis notebook, and data generation/analysis scripts for diginorm paper
Language:Python8 25 46
dib-lab/2014-paper-wssspe14
Language:TeX5 3 01
dib-lab/2016-pycon-tutorial-project
Language:Python5 12 07
dib-lab/2015-paper-10-simple-rules-releasing
4 4 33
dib-lab/2015-09-10-scihack
Inaugural Group Science Coding Session
Language:Python2 3 21
dib-lab/2015-khmer-wok2-vc
Language:Python2 2 0
dib-lab/2014-mrnaseq-cloud
Language:TeX1 28 01
dib-lab/2015-khmer-wok4-multimap
Language:Python1 2 0
dib-lab/2016-paper-p_asteroides
Language:Shell1 21 0
dib-lab/khmer-citation
The paper that is the citation handle for khmer software.
Language:TeX1 28 01
dib-lab/MMETSP
Language:Jupyter Notebook1 6 01
dib-lab/2013-lamprey
Language:TeX4 0
dib-lab/2013-paper-ssspe
4 pager for http://wssspe.researchcomputing.org.uk/
Language:TeX5 02
dib-lab/2013-read-aligner
Language:Python24 0
dib-lab/2014-mrnaseq-models
Language:TeX2 02
dib-lab/2015-07-06-ucdavis
Language:HTML7 73
dib-lab/2015-khmer-wok1-ec
Language:Python2 0
dib-lab/2015-khmer-wok3-counting
Language:Python2 0
dib-lab/2015-khmer-wok5-eval
Language:Python2 0
dib-lab/2015-petMarSB
Many-sample de novo assembly of the sea lamprey transcriptome
Language:TeX4 73
dib-lab/dib-lab.github.io
3 0
dib-lab/dib-modules
DIB lab modules for MSU HPCC
Language:Lua3 0
dib-lab/ecoli-assembly-binder
3 0
dib-lab/galaxy
Data intensive biology for everyone.
Language:Python3 0
dib-lab/khmer-testdata
Large(r) testing files that don't belong in the main khmer repository
29 0
dib-lab/tule-elk
Language:Shell
dib-lab/zaok
Language:Jupyter Notebook1
dib-lab/zen-khmer
3 0