stephenturner

oneliners

Useful bash one-liners for bioinformatics.

annotables

R data package for annotating/converting Gene IDs

qqman

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

kgp

1000 Genomes Project Metadata R Package

devnotes

Random programming notes and orphan scripts

alpinist

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

Tverse

Meta package that installs my most commonly used packages

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

pipebox

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

rpdd

R package Docker demo

string2dna

R package to encode/decode strings as nucleotide sequences

alignment-extraction

Alignment extraction

celltypist

A tool for semi-automatic cell type annotation

docker-builds

:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

dssp

Application to assign secondary structure to proteins

duckpenguins

Demonstration of a Shiny app that queries a duckdb database holding the Palmer Penguins data. The app's code was generated with a simple prompt to ChatGPT.

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

hexmake

A Shiny App for Making Hex Stickers.

mastering-shiny

Mastering Shiny: a book

MusiteDeep_web

This repository contains the stand-alone tool for MusiteDeep server

NGSNGS

NGSNGS: Next generation simulator for next generation sequencing data

phast

PHAST

pydata-book

Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media

python-mastery

Advanced Python Mastery (course by @dabeaz)

rphast

RPHAST: Phylogenetic Analysis with Space/Time Models in R

rticles

LaTeX Journal Article Templates for R Markdown

stevedore

:cloud::rowboat::whale::cloud: Docker client for R

TxDb.Cfamiliaris.UCSC.canFam3.ncbiRefSeq

TxDb for dog from UCSC NCBI RefSeq Genes

webr-ghp