jorvis
Bioinformatics guy at @IGS where my primary projects involve genome annotation (prok, euk and meta) and expression analysis. Also a grad professor at Hopkins.
Institute for Genome SciencesTulsa, OK, USA
Pinned Repositories
gEAR
The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.
Attributor
Generate gene annotation from a wide variety of evidence sources
biocode
Bioinformatics code libraries and scripts
Compacta
A fast contig clustering tool
ergatis
Ergatis is a web-based utility that is used to create, run, and monitor reusable computational analysis pipelines.
GALES
Genomic Annotation Logic and Execution System
JCVI_HMP_metagenomic_pipeline
Metagenomic functional annotation pipeline, used within the Human Microbiome Project
notebooks
pandas
Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
qtask
Quick, project-based task effort reporting from the command line.
jorvis's Repositories
jorvis/biocode
Bioinformatics code libraries and scripts
jorvis/ergatis
Ergatis is a web-based utility that is used to create, run, and monitor reusable computational analysis pipelines.
jorvis/JCVI_HMP_metagenomic_pipeline
Metagenomic functional annotation pipeline, used within the Human Microbiome Project
jorvis/GALES
Genomic Annotation Logic and Execution System
jorvis/Attributor
Generate gene annotation from a wide variety of evidence sources
jorvis/pandas
Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
jorvis/Compacta
A fast contig clustering tool
jorvis/notebooks
jorvis/qtask
Quick, project-based task effort reporting from the command line.
jorvis/radar
Interactive radar visualization
jorvis/scanpy
Single-Cell Analysis in Python. Scales to >1M cells.
jorvis/TIGR
Ancient perl modules developed at TIGR for genomic data processing, still used by some legacy code but until now passed around privately among TIGR ex-employees like the last Twinkies on earth.
jorvis/AdventOfCode
My quick(-ish) solutions to the Advent Of Code challenges
jorvis/AplysiaScripts
Utility scripts used in the generation of an annotated transcriptome of the organism Aplysia californica
jorvis/companion
Pipeline for automatic eukaryotic parasite annotation
jorvis/consultDash
jorvis/libcutter-perl
Perl library for representing and cutting shapes out of a plane (as one might do with a DIY CNC laser and sheet metal)
jorvis/Multicore-TSNE
Parallel t-SNE implementation with Python and Torch wrappers.
jorvis/PASApipeline
PASA software
jorvis/toil
A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python
jorvis/transrate
Understand your transcriptome assembly
jorvis/Trinotate
Trinotate source code
jorvis/workflows
Community maintained workflows & tools (with examples)