nhoffman/mypy

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Created almost 13 years ago
Updated almost 13 years ago

nhoffman/mypy

nhoffman

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Configuration for my python environment

argparse-bash

Use python's argparse module in shell scripts

org-export

batch export of org-mode files from the command line

bioscons

Extends the scons build tool for reproducible workflows in bioinformatics.

.emacs.d

My emacs configuration

alnvu

Reformat and condense multiple sequence alignments to highlight variability

Seq

(abandoned) python utilities for manipulation of biological sequences

swarmwrapper

Wraps swarm to perform pooled dereplication

mkvenv

A wrapper for virtualenv, pip, and wheel

rvenv

Install and manage R packages in a python virtualenv.

emacs-config

My emacs configuration, take 2

barcodecop

Enforce barcode match stringency and read quality in demultiplexed MiSeq reads

fastalite

Simplest possible fasta/fastq parser

opiates

Automated QA for a clinical LC/MS urine opaites assay

borborygmi

A blog built using emacs org-mode and Pelican

ya16sdb

A curated subset of 16S rRNA sequences from NCBI

pymenu

Provides a simple, interactive text-based user interface

unittools

Lightweight utility for running python unit tests

uwgroups

Python library and CLI for UW Groups API

16s-capture

Pipleine code for "Sensitive identification of bacterial DNA in clinical specimens by broad range 16S rRNA enrichment"

dada2-nf

A Nextflow pipeline for processing 16S rRNA sequences using dada2

ungapatchka

A python project template with bells and whistles

deduplicate

Remove duplicates from collections of biological sequences

lab-software-whitepaper

A whitepaper describing software development best practices for the clinical laboratory