Kevin Ryan's starred repositories
altanalyze
AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.
SNAF
Splicing Neo Antigen Finder (SNAF) is an easy-to-use Python package to identify splicing-derived tumor neoantigens from RNA sequencing data, it further leverages both deep learning and hierarchical Bayesian models to prioritize certain candidates for experimental validation
CATD_snakemake
Snakemake pipeline for benchmarking cell-type deconvolution methods and deconvolving real bulk RNA-seq data with the use of scRNA-seq datasets
LR-splitpipe
Demultiplexing and debarcoding tool designed for LR-Split-seq data.
ccRCC_scLongRead
This repository has the codes to reproduce the figures in our paper on single-cell long-read RNA sequencing data of patient-derived ccRCC organoids
NCOMMS_NSCLC_scFibs
Code Associated with the Nature Communications Publication entitled "Single-cell analysis reveals prognostic fibroblast subpopulations linked to molecular and immunological subtypes of lung cancer"
MixTCRpred
Predictor of TCR-epitope interactions
kourami-docker
Dockerfile for Kourami assembler for HLA haplotypes
HLA_collections
A script to run HLA typing tools from next generation sequencing data
aws-for-bioinformatics
AWS for Bioinformatics Researchers
Repo_skeleton
Default files to copy over to a new Repo
polysolver-singularity
Building a Singularity image of Polysolver
polysolver
Singularity port of HLA typing based on an input exome BAM file and is currently infers infers alleles for the three major MHC class I (HLA-A, -B, -C)
advent-of-code
My Advent of Code submissions. For 2021 and before, these are the original code I used, without any modifications after-the-fact. As such, they are probably not as efficient or short as they should be, because I want a working solution faster, not a better solution. For 2022 and after, these are the solutions uploaded to my YouTube channel.