Tom Smith

quarto-course-template. Lua

ltc-color-palettes. "ltc_palettes: Tailored for data visualization enthusiasts, ltc_palettes is an R package that offers a curated collection of color palettes. Crafted to enhance clarity and impact, these palettes ensure that your visual representations not only communicate data effectively but also aesthetically

tDRmapper. Perl

act. Run your GitHub Actions locally 🚀

UMI-tools. Tools for handling Unique Molecular Identifiers in NGS data sets

uniprotREST. UniProt REST API R wrapper

camprotR. R

snakemake-wrappers. This is the development home of the Snakemake wrapper repository, see

mamba. The Fast Cross-Platform Package Manager

drawCell. R package to create cell pictures.

RoseTTAFold. This package contains deep learning models and related scripts for RoseTTAFold

iortcw. Merge of ioquake3 features and fixes into RTCW code bases

idemuxcpp. iDemux is an all-in-one command line tool that can be used for both demultiplexing and error correction of FASTQ files. It enables demultiplexing of i1 inline barcodes of Lexogen’s QuantSeq-Pool as well as demultiplexing of i7 and/or i5 indices of any other RNA-Seq library prep. iDemux can also be used for superior error correction of RNA-Seq libraries generated with Lexogen’s UDI 12 nt Unique Dual Indices. This C++ version is faster than the Python version but requires a certain proficiency in command line tool handling.

pybktree. Python BK-tree data structure to allow fast querying of "close" matches

tidies. A Grammar of Data Manipulation for Omics Data

calib. Calib clusters barcode tagged paired-end reads based on their barcode and sequence similarity.

salmon. 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

UMI-tools_pipelines. Pipelines for re-analysis of iCLIP and scRNA-Seq data for UMI-tools publication

cgat. Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps

TeachingMaterial. Various teaching material