nhoffman/moin-labmanual

Use MoinMoin as a CMS for document control in the clinical laboratory

Language: Python - Size: 121 KB - Last synced: 4 days ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

nhoffman/borborygmi

A blog built using emacs org-mode and Pelican

Language: HTML - Size: 1.14 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 2 - Forks: 0

nhoffman/argparse-bash

Use python's argparse module in shell scripts

Language: Shell - Size: 33.2 KB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 164 - Forks: 27

nhoffman/emacs-config

My emacs configuration, take 2

Language: Emacs Lisp - Size: 305 KB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 2 - Forks: 0

nhoffman/api-2024-llm-demos

Language: Jupyter Notebook - Size: 45.9 KB - Last synced: 16 days ago - Pushed: 17 days ago - Stars: 0 - Forks: 0

nhoffman/ya16sdb

A curated subset of 16S rRNA sequences from NCBI

Language: Python - Size: 4.1 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 2 - Forks: 3

nhoffman/alnvu

Reformat and condense multiple sequence alignments to highlight variability

Language: Python - Size: 297 KB - Last synced: 3 days ago - Pushed: over 3 years ago - Stars: 7 - Forks: 3

nhoffman/org-export

batch export of org-mode files from the command line

Language: Emacs Lisp - Size: 216 KB - Last synced: 10 days ago - Pushed: 6 months ago - Stars: 61 - Forks: 17

nhoffman/bioscons

Extends the scons build tool for reproducible workflows in bioinformatics.

Language: Python - Size: 711 KB - Last synced: 4 days ago - Pushed: about 1 year ago - Stars: 17 - Forks: 4

nhoffman/16s-capture

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

Language: Python - Size: 1.02 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 0

nhoffman/lab-software-whitepaper

A whitepaper describing software development best practices for the clinical laboratory

Language: TeX - Size: 7.81 KB - Last synced: 9 months ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

nhoffman/static_html_demo

a demo for building static html reports with Jinja2 and Bootstrap

Language: Python - Size: 363 KB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0

nhoffman/argparse Fork of trevorld/r-argparse

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

Language: R - Size: 297 KB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0

nhoffman/.emacs.d

My emacs configuration

Language: Emacs Lisp - Size: 1.1 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 16 - Forks: 4

nhoffman/ungapatchka

A python project template with bells and whistles

Language: Python - Size: 67.4 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 2

nhoffman/barcodecop

Enforce barcode match stringency and read quality in demultiplexed MiSeq reads

Language: Python - Size: 400 KB - Last synced: 6 days ago - Pushed: about 1 year ago - Stars: 2 - Forks: 2

nhoffman/fastalite

Simplest possible fasta/fastq parser

Language: Python - Size: 29.3 KB - Last synced: 14 days ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

nhoffman/dash_DNA_fiber_app_v7 Fork of sshuklz/dash_DNA_fiber_app_v7

Language: Python - Size: 8.97 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

nhoffman/s3simple Fork of paulhammond/s3simple

A bash S3 client with minimal dependencies

Language: Shell - Size: 4.88 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

nhoffman/uwgroups

Python library and CLI for UW Groups API

Language: Python - Size: 488 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 1

nhoffman/PACKAGE

Language: Python - Size: 7.81 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

nhoffman/portfolio

My personal faculty portfolio site

Language: Python - Size: 4.52 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

nhoffman/xallaxtest

Language: Python - Size: 54.7 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

nhoffman/barcoder

Read barcodes from scanned documents

Language: Python - Size: 523 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

nhoffman/dada2-nf

A Nextflow pipeline for processing 16S rRNA sequences using dada2

Language: Python - Size: 22.2 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 2

nhoffman/pelicandemo

demo pelican deployed to github pages with a guthub action

Language: Python - Size: 267 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

nhoffman/singularity-rstudio Fork of nickjer/singularity-rstudio

RStudio Server in a Singularity container

Language: Python - Size: 25.4 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

nhoffman/api-standards-committee

Workspace for the Association for Pathology Informatics Standards Committee

Size: 1000 Bytes - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

nhoffman/CLOMP Fork of vpeddu/CLOMP

UW Virology's Clinically OK Metagenomic Pipeline

Language: Nextflow - Size: 1.25 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

nhoffman/zsh-cwd-history Fork of ericfreese/zsh-cwd-history

Scopes your command history to the current working directory

Size: 7.81 KB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

nhoffman/place-16s

16S rRNA sequence placement and taxonomic assignment with gappa

Language: Python - Size: 3.03 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 1

nhoffman/learn-nextflow

Experiments with Nextflow

Language: Shell - Size: 2.93 KB - Last synced: 12 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

nhoffman/hemogram Fork of sukraBhandari/hemogram

Language: JavaScript - Size: 1.1 MB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

nhoffman/oltg-embedded

Proof of concept for embedding the OLTG API

Language: HTML - Size: 10.7 KB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

nhoffman/cloudformation

Learning how to use AWS cloud formation

Language: Shell - Size: 24.4 KB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

nhoffman/flask_uwnetid Fork of nkrumm/flask_uwnetid

Language: Python - Size: 0 Bytes - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

nhoffman/dada2-cli

A command line wrapper and Dockerfile for dada2

Language: R - Size: 15.6 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 2

nhoffman/smart-on-fhir-tutorial Fork of uw-fhir/smart-on-fhir-tutorial

SMART on FHIR Tutorial for 2018 UW FHIR Workshop based on https://engineering.cerner.com/smart-on-fhir-tutorial/

Language: JavaScript - Size: 1.25 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

nhoffman/rvenv

Install and manage R packages in a python virtualenv.

Language: R - Size: 10.7 KB - Last synced: 14 days ago - Pushed: over 8 years ago - Stars: 2 - Forks: 1

nhoffman/swarmwrapper

Wraps swarm to perform pooled dereplication

Language: Python - Size: 3.21 MB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 3 - Forks: 0

nhoffman/Seq

(abandoned) python utilities for manipulation of biological sequences

Language: Python - Size: 275 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 7 - Forks: 0

nhoffman/tagit

Simple python package versioning with git tags

Language: Python - Size: 14.6 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

nhoffman/R-reporting

Docker image for generating plots and reports with R

Language: Shell - Size: 2.93 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 1

nhoffman/dockertest

A test repo for docker hub

Size: 0 Bytes - Last synced: about 1 year ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

nhoffman/ggbiplot Fork of vqv/ggbiplot

A biplot based on ggplot2

Language: R - Size: 98.6 KB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

nhoffman/bioy

Tools for NGS sequence analysis and bacterial classification

Language: UnrealScript - Size: 4.84 MB - Last synced: 9 months ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0

nhoffman/csvkit Fork of wireservice/csvkit

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

Language: Prolog - Size: 19.9 MB - Last synced: about 1 year ago - Pushed: over 10 years ago - Stars: 1 - Forks: 1

nhoffman/mkvenv

A wrapper for virtualenv, pip, and wheel

Language: Python - Size: 41 KB - Last synced: 6 days ago - Pushed: about 8 years ago - Stars: 2 - Forks: 1

nhoffman/mypy

Configuration for my python environment

Language: Shell - Size: 89.8 KB - Last synced: about 1 year ago - Pushed: about 12 years ago - Stars: 1 - Forks: 0

nhoffman/deltas

Code and data for delta check simulation paper

Language: Shell - Size: 3.62 MB - Last synced: about 1 year ago - Pushed: about 10 years ago - Stars: 0 - Forks: 0

nhoffman/deduplicate

Remove duplicates from collections of biological sequences

Size: 113 KB - Last synced: about 1 year ago - Pushed: about 13 years ago - Stars: 1 - Forks: 0

nhoffman/pplacer Fork of matsen/pplacer

Phylogenetic placement and downstream analysis

Language: OCaml - Size: 11.8 MB - Last synced: about 1 year ago - Pushed: over 10 years ago - Stars: 0 - Forks: 0

nhoffman/scons_template

scons template for reproducible research

Language: Shell - Size: 121 KB - Last synced: about 1 year ago - Pushed: over 10 years ago - Stars: 0 - Forks: 0

nhoffman/opiates

Automated QA for a clinical LC/MS urine opaites assay

Language: Python - Size: 652 KB - Last synced: about 1 year ago - Pushed: over 11 years ago - Stars: 1 - Forks: 0

nhoffman/pymenu

Provides a simple, interactive text-based user interface

Language: Python - Size: 376 KB - Last synced: about 1 year ago - Pushed: about 13 years ago - Stars: 2 - Forks: 1

nhoffman/blog

(yet another) org-mode blogging framework

Language: Emacs Lisp - Size: 126 KB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0

nhoffman/unittools

Lightweight utility for running python unit tests

Language: Python - Size: 93.8 KB - Last synced: about 1 year ago - Pushed: over 13 years ago - Stars: 2 - Forks: 0

nhoffman/deenurp Fork of fhcrc/deenurp

De-novo selection of reference sequences

Language: Python - Size: 588 KB - Last synced: about 1 year ago - Pushed: about 11 years ago - Stars: 0 - Forks: 0

nhoffman/seqlabd Fork of madhadron/seqlabd

Daemon for the clinical sequencing lab at UWMC

Language: Python - Size: 1.68 MB - Last synced: about 1 year ago - Pushed: about 12 years ago - Stars: 1 - Forks: 0

nhoffman/nestly Fork of fhcrc/nestly

Make and use nested directory trees corresponding to combinatorial choices of parameters

Language: Python - Size: 225 KB - Last synced: about 1 year ago - Pushed: over 12 years ago - Stars: 1 - Forks: 0