Stephen Turner

oneliners. Useful bash one-liners for bioinformatics.

qqman. An R package for creating Q-Q and manhattan plots from GWAS results

annotables. R data package for annotating/converting Gene IDs

biorecap. Retrieve and summarize bioRxiv preprints with a local LLM using ollama

twitterchive. Archive and analyze results from a Twitter search (**no longer maintained**)

adapters. Adapters for trimming

solarplot. Mitochondrial Solar Plot

kgp. 1000 Genomes Project Metadata R Package

mergelanes. Merge fastq files split over lanes

msigdf. Molecular Signatures Database (MSigDB) in a data frame

hcop. HGNC Comparison of Orthology Predictions (HCOP)

Tverse. Meta package that installs my most commonly used packages

workshops. Biological Data Science Workshops

deseq-to-fgsea. HTML

repo2txt. Web-based tool converts GitHub repository contents into a single formatted text file

devnotes. Random programming notes and orphan scripts

monthsheets. R

covcalc. Coverage / read count calculator for sequencing experiments

lifeweeks. Visualize your life in weeks

alpinist. Alpine Linux image with R, a subset of Tidyverse packages, and domain-specific tools for genomic data manipulation and analysis.

slimbioinfo. Lightweight Alpine-based Docker images for common bioinformatics tools

docker101. Dockerfile

bdsr. Biological Data Science with R

om..bcftools. outsider-module: bcftools

trailprofile. Charlottesville Area Trail Profiles

rpdd. R package Docker demo

biorxivbsky. Chrome extension to share bioRxiv papers to Bluesky

drawmydata. A webpage for teaching that lets you make a dataset by clicking in a blank scatterplot

Tmisc. Miscellaneous utility functions for data manipulation, data tidying, and working with gene expression data and biological sequence data.

dstt-rmd. CSTE DSTT RMarkdown demo

ganttrify. Create beautiful Gantt charts with ggplot2

playground_rpkg_demo. Example R package built by Positron Assistant with Claude 4 Sonnet in Agent mode

NgsRelate. C++

rsidx. Library for indexing VCF files for random access searches by rsID

rstudio-snippets. My custom RStudio snippets

clinvar. This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file.

free-for-dev. A list of SaaS, PaaS and IaaS offerings that have free tiers of interest to devops and infradev

pipebox. Bioinformatics pipeline in a box (demonstration containerizing workflows with Docker)

dsttbook. Data Science Team Training

caffeinated. Provide statistics about your caffeine level specifically when you'd be going to bed.

rmarkdown-crossreferences. Cross-reference figures and tables using plain RMarkdown

bioinf-bloggers. A planet-like static website to track bioinformatics blogs around the world

docker-builds. :package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

gi2017software. Software from GI2017

string2dna. R package to encode/decode strings as nucleotide sequences

rphast. RPHAST: Phylogenetic Analysis with Space/Time Models in R

shc. shc - Generic shell script compiler