nhoffman Goto Github PK

.emacs.d

My emacs configuration

16s-capture

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

alnvu

Reformat and condense multiple sequence alignments to highlight variability

api-2024-llm-demos

api-standards-committee

Workspace for the Association for Pathology Informatics Standards Committee

argparse

R package providing a command line optional and positional argument parser.

argparse-bash

Use python's argparse module in shell scripts

barcodecop

Enforce barcode match stringency and read quality in demultiplexed MiSeq reads

barcoder

Read barcodes from scanned documents

bioscons

Extends the scons build tool for reproducible workflows in bioinformatics.

bioy

Tools for NGS sequence analysis and bacterial classification

blog

(yet another) org-mode blogging framework

borborygmi

A blog built using emacs org-mode and Pelican

clomp

UW Virology's Clinically OK Metagenomic Pipeline

cloudformation

Learning how to use AWS cloud formation

csvkit

A suite of utilities for converting to and working with CSV, the king of tabular file formats.

dada2-cli

A command line wrapper and Dockerfile for dada2

dada2-nf

A Nextflow pipeline for processing 16S rRNA sequences using dada2

dash_dna_fiber_app_v7

deduplicate

Remove duplicates from collections of biological sequences

deenurp

De-novo selection of reference sequences

deltas

Code and data for delta check simulation paper

dockertest

A test repo for docker hub

emacs-config

My emacs configuration, take 2

fastalite

Simplest possible fasta/fastq parser

flask_uwnetid

ggbiplot

A biplot based on ggplot2

hemogram

lab-software-whitepaper

A whitepaper describing software development best practices for the clinical laboratory

learn-nextflow

Experiments with Nextflow