jorvis

biocode

Bioinformatics code libraries and scripts

ergatis

Ergatis is a web-based utility that is used to create, run, and monitor reusable computational analysis pipelines.

JCVI_HMP_metagenomic_pipeline

Metagenomic functional annotation pipeline, used within the Human Microbiome Project

GALES

Genomic Annotation Logic and Execution System

Attributor

Generate gene annotation from a wide variety of evidence sources

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

Compacta

A fast contig clustering tool

notebooks

qtask

Quick, project-based task effort reporting from the command line.

radar

Interactive radar visualization

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

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.

AdventOfCode

My quick(-ish) solutions to the Advent Of Code challenges

AplysiaScripts

Utility scripts used in the generation of an annotated transcriptome of the organism Aplysia californica

companion

Pipeline for automatic eukaryotic parasite annotation

consultDash

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)

Multicore-TSNE

Parallel t-SNE implementation with Python and Torch wrappers.

PASApipeline

PASA software

toil

A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python

transrate

Understand your transcriptome assembly

Trinotate

Trinotate source code

workflows

Community maintained workflows & tools (with examples)