KarchinLab

open-cravat

A modular annotation tool for genomic variants

2020plus

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

bigmhc

BigMHC predicts MHC-I (neo)epitope presentation and immunogenicity

mhcnuggets

MHC Class I and Class II neoantigen binding prediction

SCHISM

Subclonal Hierarchy Inference from Somatic Mutations

HotMAPS

Detects hotspot regions for somatic mutations in 3D protein structures

HotMAPS_2016

Detects hotspot regions for somatic mutations in 3D protein structures

CHASMplus

Predicts which missense mutations will drive growth of human cancers

probabilistic2020

Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test

pictograph

A Bayesian hierarchical model to build tumor evolutionary trees

Tokheim_Cell_Systems_2019

Data analysis for the CHASMplus paper

open-cravat-multiuser

opencravat-cwl

HLA-Mediated-Tumor-Immunogenicity-Manuscript

open-cravat-modules-karchinlab

BOMP

MOCA

Multivariate Organization of Combinatorial Alterations

open-cravat-dxapp

open-cravat-dxapp

open-cravat-readthedocs

3D-CLUMP

APM-Clustering-ICB-Manuscript

civic-opencravat-2023

Code from the 2023 CiVIC Hackathon

manta

Structural variant and indel caller for mapped sequencing data

MosaicSim

fork of MosaicSim developed by CMUSchwartzlab

OC-cloudform

Cloudformation templating for OpenCravat AWS pipeline with automated processing and upload to S3 bucket

open-cravat-cloudqueue

Scalable system for running OpenCRAVAT on GCP

open-cravat-extras

open-cravat-store

open-data-registry

A registry of publicly available datasets on AWS

TCRtoolkit

A NextFlow pipeline for processing, analyzing, and visualizing bulk TCR sequencing data.