Pinned Repositories
taxtastic
Create and maintain phylogenetic "reference packages" of biological sequences.
.emacs.d
My emacs configuration
alnvu
Reformat and condense multiple sequence alignments to highlight variability
argparse-bash
Use python's argparse module in shell scripts
bioscons
Extends the scons build tool for reproducible workflows in bioinformatics.
dada2-nf
A Nextflow pipeline for processing 16S rRNA sequences using dada2
org-export
batch export of org-mode files from the command line
Seq
(abandoned) python utilities for manipulation of biological sequences
ya16sdb
A curated subset of 16S rRNA sequences from NCBI
nhoffman's Repositories
nhoffman/argparse-bash
Use python's argparse module in shell scripts
nhoffman/org-export
batch export of org-mode files from the command line
nhoffman/bioscons
Extends the scons build tool for reproducible workflows in bioinformatics.
nhoffman/.emacs.d
My emacs configuration
nhoffman/alnvu
Reformat and condense multiple sequence alignments to highlight variability
nhoffman/barcodecop
Enforce barcode match stringency and read quality in demultiplexed MiSeq reads
nhoffman/borborygmi
A blog built using emacs org-mode and Pelican
nhoffman/emacs-config
My emacs configuration, take 2
nhoffman/fastalite
Simplest possible fasta/fastq parser
nhoffman/pymenu
Provides a simple, interactive text-based user interface
nhoffman/ya16sdb
A curated subset of 16S rRNA sequences from NCBI
nhoffman/16s-capture
Pipleine code for "Sensitive identification of bacterial DNA in clinical specimens by broad range 16S rRNA enrichment"
nhoffman/lab-software-whitepaper
A whitepaper describing software development best practices for the clinical laboratory
nhoffman/uwgroups
Python library and CLI for UW Groups API
nhoffman/dada2-nf
A Nextflow pipeline for processing 16S rRNA sequences using dada2
nhoffman/api-2024-llm-demos
nhoffman/api-standards-committee
Workspace for the Association for Pathology Informatics Standards Committee
nhoffman/barcoder
Read barcodes from scanned documents
nhoffman/CLOMP
UW Virology's Clinically OK Metagenomic Pipeline
nhoffman/dash_DNA_fiber_app_v7
nhoffman/hemogram
nhoffman/learn-nextflow
Experiments with Nextflow
nhoffman/PACKAGE
nhoffman/pelicandemo
demo pelican deployed to github pages with a guthub action
nhoffman/philter-ucsf
Open source clinical text de-identification
nhoffman/place-16s
16S rRNA sequence placement and taxonomic assignment with gappa
nhoffman/portfolio
My personal faculty portfolio site
nhoffman/s3simple
A bash S3 client with minimal dependencies
nhoffman/singularity-rstudio
RStudio Server in a Singularity container
nhoffman/xallaxtest