CD2H gitForager

Jason Stajich

Login: hyphaltip

Company: University of California-Riverside

Location: Riverside

Bio: Faculty member working primarily on fungal evolution using genomic tools. Development of comparative genomics and bioinformatics tools and training.

Blog: http://lab.stajich.org/

Member of

Repositories

Annocript: Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission. It gives information about the longest ORF (using DNA2PEP) and non-coding potential of the sequences (using Portrait). A final heuristic makes Annocript to identify putative long non-coding RNAs among your transcripts.
AoC15: Advent of Code 2015
ASTRAL: Accurate Species TRee ALgorithm
autovectorscreen: Process vectorscreening locally
bcbb: Useful bioinformatics code, primarily in Python and R
BINF_toolkit: Handy scripts for routine bioinformatic analysis
Binning: Scripts required to calculate tetramer frequencies and create input files for ESOM. See: Dick, G.J., A. Andersson, B.J. Baker, S.S. Simmons, B.C. Thomas, A.P. Yelton, and J.F. Banfield (2009). Community-wide analysis of microbial genome sequence signatures. Genome Biology, 10: R85
bioperl-db: BioPerl BioSQL ORM
bioperl-run: BioPerl wrappers
biopython: Official git repository for Biopython (converted from CVS)
blobtools: Application for the visualisation of draft genome assemblies and general QC
bwa: Burrow-Wheeler Aligner
cndtools: fork of cndtools
CNVnator: a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
cocci_repeats: Coccidioides repeat analysis
Contentious_relationships_Code: Code from Shen et al Nat Eco Evo 2017
CSHL_NGS: NGS DNA analysis for the CSHL 2012 Programming for Biology course
CV: My CV
dart: DNA, Amino Acid and RNA Tests
disopred: Protein structural disorder prediction
ExaML: Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI
filo: Useful FILe and stream Operations
funannotate: Fungal genome annotation scripts
fungalgenomes.org: Supporting fungalgenomes.org website
fungaltools: Misc scripts for fungal tools, mostly for use in papers
fungidb-tools: Scripts to manage fungidb.org
fungi-gene-prediction-params: Provide trained gene prediction parameters for Fungal genome annotation
GBrowse: Unofficial prototype git repo for GBrowse. Subject to change without notice.
GEN220_2015: GEN220 course, Fall 2015 edition
gene2product: Curated list of gene names and product descriptions that pass NCBI genome submission rules.
genome-scripts: Genome Scripts used in fungal comparative genomics
H3K27: H3K27 neurospora project
homebrew-science: :snowflake: Scientific formulae for Homebrew and Linuxbrew (legacy)
htbda_perl_class: High Throughput Biological Data Analysis using Perl
hyphaltip.github.com: GitHub home for hyphaltip
impala: null
intermine: A powerful open source data warehouse system
kallisto: Near-optimal RNA-Seq quantification
khmer: in-memory k-mer counting
landslide: Generate a slideshow using the slides that power the html5-slides presentation
macports: My local macports files
MediaWiki-Extension--UserAdmin: UserAdmin is a MediaWiki extension which allows administrators to add and delete users, change user passwords, edit user details, edit user groups, resend emails (e.g. reset password email or welcome message email).
MG-RASTv4: next generation metagenome analysis
MicrobeDB: Provides a local database of all completed genomes for Bacteria and Archaea from NCBI
mobedac-fungi: MOBeDAC Fungi Database
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mTEA: Mosquito TE Annotation
neolecta: neolecta annotation and analysis
npScarf: null
otu_cluster: Cluster OTUs based on % similarity, mostly scripts to pipeline into other tools
pan-fungal-project: A Pan-Fungal Genomes Database
parsnp: null
PhyloSift: Phylogenetic and taxonomic analysis for genomes and metagenomes
PhylOTU: PhylOTU identifies microbial OTUs from metagenomic data
planets: test planets
redundans: Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
RelocaTE: Find the locations of TEs using the TSD in unassembled short reads by comparing to a closely related reference genome assembly
RelocaTE2: RelocaTE2
rhizobia-genomics: Scripts to support bacterial genomics project
runnning_blast: Demo for Derreck
SeqPrep: Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
sga: experimental de novo sequence assembler using string graphs
short-read-db: Database for shortreads and comparing overlap with genomic features
standard-RAxML: null
subopt-kaks: Suboptimal alignments and Ka, Ks calculations
systemPipeRdata: NGS workflow templates and sample data
TEamRice: Rice TE project
test_gen220_fun: null
thesis: Perl Code from my Thesis (2006)
trinityrnaseq: Trinity RNA-Seq de novo transcriptome assembly
ucr-biocluster-scripts: UCR Biocluster job scripts
ufits: Fungal ITS Clustering Package
vcflib: a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
Workshop: null

Commits To

Repository	Most Recent Commit	# Commits
hyphaltip/genome-scripts	2017-12-13 05:29:18.0	416
stajichlab/bd_popgen	2016-02-29 04:51:10.0	36
fungidb/exserohilum	2014-06-02 05:51:03.0	3
stajichlab/Candida_lusitaniae	2017-09-20 19:03:55.0	20
stajichlab/Comparative_pipeline	2017-11-09 06:04:19.0	91
zygolife/Mucormycota_comparative	2017-04-17 22:25:37.0	6
stajichlab/Cauris_popgenomics	2017-05-18 18:45:46.0	47
stajichlab/Rstol_popgenomics	2017-07-08 21:17:49.0	6

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.