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fast5seek

Subset of fast5 files contained in a fastq, BAM, or SAM file.

foldvis

Protein visualization without the pain

fpinscala

Code, exercises, answers, and hints to go along with the book "Functional Programming in Scala"

funk-svd

:zap: A python fast implementation of the famous SVD algorithm popularized by Simon Funk during Netflix Prize

gcgc

An ML-feature processing library for biological sequences.

gitignore

A collection of useful .gitignore templates

gojsondiff

Go JSON Diff

hamstring

Tools for generating and decoding error-correcting DNA barcodes

hmmpy

A Pure-Python parser of HMMER3 output

holey

finding holes in big data

ibm3202

Google Colab Tutorials for IBM3202

ideel

Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes

interacdome

Compute Site-Based Ligand-Binding Frequencies across the InteracDome

isolate_pe

Quick assembly of microbial isolates + some downstream processing

jax-unirep

Reimplementation of the UniRep protein featurization model.

json2csv

command line tool to convert json to csv

jsonschema

An(other) implementation of JSON Schema for Python

klebsiella

Rethinking an outbreak of carbapenemase-producing Klebsiella pneumoniae using hybrid nanopore sequencing

laptop

A shell script to set up a macOS laptop for web and mobile development.

learning-machine-learning

A self-help seminar for people with mild to severe machine learning disabilities.

marine-phage-paper-scripts

master-thesis

Master thesis with code and data.

metagenomics-index-correction

metagraph

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

micnet

A neural net to predict antimicrobial susceptibility from microscopy images

mock_no_input

A minimal workflow for testing that does not require input files

mock_pe

mocks

Files for testing

nanocomb

a lightweight database to search, combine and share microbial data

nanoflow

Bioinformatics pipeline for nanopore sequencing data