Our basic allele specific analysis pipeline for single nuclei data, based on nextflow

Accompanying codes for pan cancer atlas of intracellular tumor antigens

dockerization of phlat hla typing tool

Nextflow pipeline to run somatic alteration calling from single-cell data using SComatic

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Pipeline to detect HLA disruption from WES and RNAseq data

Detection of chimeric transcripts (aka fusions) from barcoded single cell RNA-seq

Plot structural variant signals from many BAMs and CRAMs

The nimble & robust variant annotator

xHLA: Fast and accurate HLA typing from short read sequence data

Deep semi-supervised complete cell deconvolution https://imsb-uke.github.io/DISSECT/

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 …

Long-read splice alignment with high accuracy

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…

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

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

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

R package for analysing single cell data

LongSom tool for long-reads

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

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

Code Associated with the Nature Communications Publication entitled "Single-cell analysis reveals prognostic fibroblast subpopulations linked to molecular and immunological subtypes of lung cancer"

Predictor of TCR-epitope interactions

Dockerfile for Kourami assembler for HLA haplotypes

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