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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

attributor

Generate gene annotation from a wide variety of evidence sources

biocode

Bioinformatics code libraries and scripts

compacta

A fast contig clustering tool

companion

Pipeline for automatic eukaryotic parasite annotation

consultdash

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

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.

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

pasapipeline

PASA software

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.

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)