Pinned Repositories
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
CHASMplus
Predicts which missense mutations will drive growth of human cancers
CLUMP
CLUstering by Mutation Position
mhcnuggets
MHC Class I and Class II neoantigen binding prediction
open-cravat
A modular annotation tool for genomic variants
open-cravat-dxapp
open-cravat-dxapp
pictograph
A Bayesian hierarchical model to build tumor evolutionary trees
probabilistic2020
Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test
SCHISM
Subclonal Hierarchy Inference from Somatic Mutations
KarchinLab's Repositories
KarchinLab/open-cravat
A modular annotation tool for genomic variants
KarchinLab/2020plus
Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
KarchinLab/bigmhc
BigMHC predicts MHC-I (neo)epitope presentation and immunogenicity
KarchinLab/mhcnuggets
MHC Class I and Class II neoantigen binding prediction
KarchinLab/CHASMplus
Predicts which missense mutations will drive growth of human cancers
KarchinLab/probabilistic2020
Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test
KarchinLab/pictograph
A Bayesian hierarchical model to build tumor evolutionary trees
KarchinLab/Tokheim_Cell_Systems_2019
Data analysis for the CHASMplus paper
KarchinLab/HotMAPS_2016
Detects hotspot regions for somatic mutations in 3D protein structures
KarchinLab/open-cravat-multiuser
KarchinLab/opencravat-cwl
KarchinLab/HLA-Mediated-Tumor-Immunogenicity-Manuscript
KarchinLab/open-cravat-readthedocs
KarchinLab/3D-CLUMP
KarchinLab/HotMAPS
KarchinLab/open-cravat-dxapp
open-cravat-dxapp
KarchinLab/open-cravat-modules-karchinlab
KarchinLab/TCRtoolkit-Bulk
A NextFlow pipeline for processing and analyzing TCRseq data
KarchinLab/APM-Clustering-ICB-Manuscript
KarchinLab/civic-opencravat-2023
Code from the 2023 CiVIC Hackathon
KarchinLab/manta
Structural variant and indel caller for mapped sequencing data
KarchinLab/MosaicSim
fork of MosaicSim developed by CMUSchwartzlab
KarchinLab/OC-cloudform
Cloudformation templating for OpenCravat AWS pipeline with automated processing and upload to S3 bucket
KarchinLab/oc_vignettes
KarchinLab/open-cravat-cloudqueue
Scalable system for running OpenCRAVAT on GCP
KarchinLab/open-cravat-extras
KarchinLab/open-cravat-roadmap
KarchinLab/open-cravat-store
KarchinLab/open-data-registry
A registry of publicly available datasets on AWS
KarchinLab/TCRtoolkit-SC
A NextFlow pipeline to process, analyze, and visualize single cell TCRseq data