KarchinLab

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41 repositories

TCRtoolkit-Bulk
Public
A NextFlow pipeline for processing and analyzing TCRseq data
Python
•1•0•0•0•Updated Dec 19, 2024Dec 19, 2024
open-cravat-modules-karchinlab
Public
JavaScript
•
MIT License
•7•0•1•1•Updated Dec 18, 2024Dec 18, 2024
open-cravat
Public
A modular annotation tool for genomic variants
javascript python bioinformatics genomics python3 bioinformatics-pipeline annotation-tool variant-annotations variant-annotation variant-analysis
JavaScript
•
MIT License
•28•116•29•0•Updated Dec 17, 2024Dec 17, 2024
open-cravat-readthedocs
Public
Python
•4•1•1•0•Updated Dec 10, 2024Dec 10, 2024
open-cravat-multiuser
Public
JavaScript
•2•2•1•1•Updated Nov 19, 2024Nov 19, 2024
open-cravat-extras
Public
Python
•
MIT License
•0•0•0•0•Updated Nov 12, 2024Nov 12, 2024
open-cravat-roadmap
Public
0•0•8•0•Updated Oct 29, 2024Oct 29, 2024
pictograph
Public
A Bayesian hierarchical model to build tumor evolutionary trees
R
•0•5•5•1•Updated Oct 21, 2024Oct 21, 2024
oc_vignettes
Public
JavaScript
•0•0•0•0•Updated Sep 13, 2024Sep 13, 2024
CHASMplus
Public
Predicts which missense mutations will drive growth of human cancers
Python
•3•11•1•1•Updated Aug 4, 2024Aug 4, 2024
2020plus
Public
Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
bioinformatics driver-genes random-forest cancer somatic-variants
Python
•
Apache License 2.0
•17•49•11•1•Updated Aug 3, 2024Aug 3, 2024
Tokheim_Cell_Systems_2019
Public
Data analysis for the CHASMplus paper
Jupyter Notebook
•4•3•0•1•Updated Jun 3, 2024Jun 3, 2024
TCRtoolkit-SC
Public
A NextFlow pipeline to process, analyze, and visualize single cell TCRseq data
Nextflow
•0•0•0•0•Updated May 18, 2024May 18, 2024
open-cravat-dxapp
Public
open-cravat-dxapp
Python
•0•0•1•0•Updated May 6, 2024May 6, 2024
bigmhc
Public
BigMHC predicts MHC-I (neo)epitope presentation and immunogenicity
Jupyter Notebook
•
Other
•10•47•1•1•Updated Apr 23, 2024Apr 23, 2024
HotMAPS_2016
Public
Detects hotspot regions for somatic mutations in 3D protein structures
hotspot cancer protein-structure somatic-mutations hotspot-regions missense-mutations exome-scale
Python
•
Apache License 2.0
•0•2•5•0•Updated Mar 12, 2024Mar 12, 2024
OC-cloudform
Public
Cloudformation templating for OpenCravat AWS pipeline with automated processing and upload to S3 bucket
Python
•1•0•0•0•Updated Feb 14, 2024Feb 14, 2024
HotMAPS
Public
Python
•0•0•1•0•Updated Dec 29, 2023Dec 29, 2023
3D-CLUMP
Public
Python
•
MIT License
•0•0•0•0•Updated Nov 21, 2023Nov 21, 2023
MosaicSim
Public
fork of MosaicSim developed by CMUSchwartzlab
Jupyter Notebook
•
MIT License
•1•0•0•0•Updated Sep 6, 2023Sep 6, 2023
civic-opencravat-2023
Public
Code from the 2023 CiVIC Hackathon
Python
•0•0•0•0•Updated Aug 12, 2023Aug 12, 2023
probabilistic2020
Public
Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test
bioinformatics cancer somatic-variants driver-genes oncogene tumor-suppressor-gene
Python
•
Apache License 2.0
•5•8•2•2•Updated Jul 6, 2023Jul 6, 2023
mhcnuggets
Public
MHC Class I and Class II neoantigen binding prediction
Python
•
Other
•10•26•9•0•Updated Mar 17, 2023Mar 17, 2023
open-data-registry
Public
A registry of publicly available datasets on AWS
Python
•
Apache License 2.0
•931•0•0•0•Updated Jan 12, 2023Jan 12, 2023
APM-Clustering-ICB-Manuscript
Public
R
•1•0•0•0•Updated Jan 2, 2023Jan 2, 2023
manta
Public
Structural variant and indel caller for mapped sequencing data
C++
•
GNU General Public License v3.0
•153•0•0•0•Updated Dec 21, 2022Dec 21, 2022
HLA-Mediated-Tumor-Immunogenicity-Manuscript
Public
R
•1•1•0•0•Updated Apr 20, 2022Apr 20, 2022
open-cravat-store
Public
Python
•0•0•0•0•Updated Mar 30, 2022Mar 30, 2022
open-cravat-cloudqueue
Public
Scalable system for running OpenCRAVAT on GCP
Python
•
GNU General Public License v3.0
•1•0•0•0•Updated Jul 31, 2021Jul 31, 2021
opencravat-cwl
Public
Common Workflow Language
•0•2•0•0•Updated Sep 23, 2020Sep 23, 2020