kevinpryan

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.

rmats-turbo

aws-for-bioinformatics

AWS for Bioinformatics Researchers

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.

ultra

Long-read splice alignment with high accuracy

IRFinder

Detecting intron retention from RNA-Seq experiments

deTiN

DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.

speckle

R package for analysing single cell data

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

kourami

Kourami: Graph-guided assembly for HLA alleles

pocp

Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.

LR-splitpipe

Demultiplexing and debarcoding tool designed for LR-Split-seq data.

CATD_snakemake

Snakemake pipeline for benchmarking cell-type deconvolution methods and deconvolving real bulk RNA-seq data with the use of scRNA-seq datasets

scywalker

A program for the analysis of single cell nanopore long read data

GLASSx

GLASS consortium

MixTCRpred

Predictor of TCR-epitope interactions

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)

polysolver-singularity

Building a Singularity image of Polysolver

ScanNeo2

Snakemake-based computational workflow for neoantigen prediction from diverse sources

Repo_skeleton

Default files to copy over to a new Repo

HLA_collections

A script to run HLA typing tools from next generation sequencing data

CAFclassification

DICAST

Docker Integrated Comparison of Alternative Splicing (AS) Tools. Benchmarking AS tools and genomic alignment tools.

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"

LongSom

LongSom tool for long-reads

mhc_genotyping

MOI--An-integrated-solution-for-omics-analyses

kourami-docker

Dockerfile for Kourami assembler for HLA haplotypes

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

project-scripts-