jgrundstad
Head of Genomics Research Center Bioinformatics Engineering at AbbVie (Thoughts and opinions are my own, and not AbbVie's)
AbbVieNorth Chicago, IL
Pinned Repositories
alignment2
Will evolve to the new alignment pipeline to be run on cloud instead of cluster
coverage_analysis
Tools for inspecting Illumina sequence alignment coverage
flask
A microframework based on Werkzeug, Jinja2 and good intentions
genotyping
Commonly used scripts for performing genotyping and annotation
hgac-glacier
scripts for backing up HGAC run directories to glacier
hgac_preprocessing
Illumina preprocessing daemon
mouse_filter
Filter mouse reads from a Human PDX derrived .bam
pheweb
A tool to build multi-phenotype GWAS browsers
Variant_Report_Viewer
Web application to load, annotate, parse, search, and display VCF data
jgrundstad's Repositories
jgrundstad/mouse_filter
Filter mouse reads from a Human PDX derrived .bam
jgrundstad/pheweb
A tool to build multi-phenotype GWAS browsers
jgrundstad/Variant_Report_Viewer
Web application to load, annotate, parse, search, and display VCF data
jgrundstad/alignment2
Will evolve to the new alignment pipeline to be run on cloud instead of cluster
jgrundstad/coverage_analysis
Tools for inspecting Illumina sequence alignment coverage
jgrundstad/flask
A microframework based on Werkzeug, Jinja2 and good intentions
jgrundstad/genotyping
Commonly used scripts for performing genotyping and annotation
jgrundstad/hgac-glacier
scripts for backing up HGAC run directories to glacier
jgrundstad/hgac_preprocessing
Illumina preprocessing daemon
jgrundstad/igsb_qc_couchdb
Tools for interacting with the IGSB alignment QC CouchDB
jgrundstad/igsb_ucsc-tracks
Select subsets of available .bw files on the IGSB Hub for viewing in the UCSC Genome Browser
jgrundstad/jg_bash_env
bash environment files
jgrundstad/KLC_tracker
jgrundstad/MediaLibraryCondenser
Search a given set of directory locations for media files, and provide options for removing duplicates.
jgrundstad/ngs_qc_scripts
Collection of my commonly used scripts for generating QC alignments for NextGenSequencing data.
jgrundstad/PDC_scripts
Scripts for interacting with OpenStack
jgrundstad/qc_stats
Custom qc stats parsing and reporting for IGSB NGS projects
jgrundstad/SAIGEgds
Scalable Implementation of Generalized mixed models using GDS files
jgrundstad/viewer
IGSB Variant Report Viewer