Projects in Awesome Lists by KarchinLab
A curated list of projects in awesome lists by KarchinLab .
https://github.com/KarchinLab/open-cravat
A modular annotation tool for genomic variants
annotation-tool bioinformatics bioinformatics-pipeline bioinformatics-tool genomic-data-analysis genomics javascript python python3 variant-analysis variant-annotation variant-annotations
Last synced: 16 Nov 2025
https://github.com/karchinlab/open-cravat
A modular annotation tool for genomic variants
annotation-tool bioinformatics bioinformatics-pipeline bioinformatics-tool genomic-data-analysis genomics javascript python python3 variant-analysis variant-annotation variant-annotations
Last synced: 16 May 2025
https://github.com/karchinlab/2020plus
Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
bioinformatics cancer driver-genes random-forest somatic-variants
Last synced: 16 Mar 2025
https://github.com/karchinlab/bigmhc
BigMHC predicts MHC-I (neo)epitope presentation and immunogenicity
Last synced: 16 Mar 2025
https://github.com/karchinlab/mhcnuggets
MHC Class I and Class II neoantigen binding prediction
Last synced: 17 Oct 2025
https://github.com/karchinlab/schism
Subclonal Hierarchy Inference from Somatic Mutations
Last synced: 16 Mar 2025
https://github.com/karchinlab/chasmplus
Predicts which missense mutations will drive growth of human cancers
Last synced: 12 Mar 2026
https://github.com/karchinlab/probabilistic2020
Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test
bioinformatics cancer driver-genes oncogene somatic-variants tumor-suppressor-gene
Last synced: 16 Mar 2025
https://github.com/karchinlab/pictograph
A Bayesian hierarchical model to build tumor evolutionary trees
Last synced: 05 Mar 2026
https://github.com/karchinlab/tokheim_pnas_2016
Evaluation protocol for computational methods predicting cancer driver genes
Last synced: 07 Jul 2025
https://github.com/karchinlab/tokheim_cell_systems_2019
Data analysis for the CHASMplus paper
Last synced: 16 Mar 2025
https://github.com/karchinlab/cancerseqstudy
Analysis of statistical power and false positives for cancer exome sequencing studies
Last synced: 14 Jun 2025
https://github.com/karchinlab/hotmaps_2016
Detects hotspot regions for somatic mutations in 3D protein structures
cancer exome-scale hotspot hotspot-regions missense-mutations protein-structure somatic-mutations
Last synced: 20 Jul 2025
https://github.com/karchinlab/tcrtoolkit-bulk
A NextFlow pipeline for processing and analyzing TCRseq data
Last synced: 26 Jul 2025
https://github.com/karchinlab/cravat-aux
test engine and test cases for CRAVATMuPIT on docker
Last synced: 16 Mar 2025
https://github.com/karchinlab/collin-thesis
Thesis: A computational search for mutational drivers of cancer
Last synced: 03 Jan 2026
https://github.com/karchinlab/open-cravat-cloudqueue
Scalable system for running OpenCRAVAT on GCP
Last synced: 15 Jul 2025
https://github.com/karchinlab/tcrtoolkit-sc
A NextFlow pipeline to process, analyze, and visualize single cell TCRseq data
Last synced: 17 Feb 2026
https://github.com/karchinlab/civic-opencravat-2023
Code from the 2023 CiVIC Hackathon
Last synced: 03 Jan 2026
https://github.com/karchinlab/moca
Multivariate Organization of Combinatorial Alterations
Last synced: 03 Jan 2026
https://github.com/karchinlab/tcrtoolkit
A NextFlow pipeline for processing, analyzing, and visualizing bulk TCR sequencing data.
Last synced: 14 Jun 2025