Lists (1)
Stars
Analysis scripts and notebooks for Numbat paper
The best free and open-source automated time tracker. Cross-platform, extensible, privacy-focused.
Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
A tool for detecting somatic variants in single cell data
Neural Networks: Zero to Hero
Draw phylogenetic trees of tumor evolution
Github for files currently published in the IPD-IMGT/HLA FTP Directory hosted at the European Bioinformatics Institute
Code accompanying The Evolutionary history of 2,658 cancers
Efficient genotyping bi-allelic SNPs on single cells
Haplotype-aware CNV analysis from single-cell RNA-seq
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
Principal analysis code used in for analysis of single cell RNAseq of primary untreated colon cancer. As described in: "Spatially organized multicellular immune hubs in human colorectal cancer"
Strelka2 germline and somatic small variant caller
Tool to convert variants to mutated peptide sequences
Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".
A library for creating complex UpSet plots with ggplot2 geoms
R package for detecting doublets in single-cell RNA sequencing data
Code relating to http://dx.doi.org/10.2139/ssrn.4132721
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
NicheNet: predict active ligand-target links between interacting cells
A thorough tutorial on HLA imputation and association, accompanying our manuscript "Tutorial: A statistical genetics guide to identifying HLA alleles driving complex disease"