UCLA JCCC - Cancer Data Science

All

80 repositories

pipeline-StableLift
Public
Nextflow pipeline for predicting variant stability across reference genome builds.
R
•
GNU General Public License v2.0
•0•0•0•1•Updated Aug 19, 2025Aug 19, 2025
pipeline-call-gSNP
Public
Nextflow pipeline to call germline short variants using GATK
pipeline nextflow
Nextflow
•
GNU General Public License v2.0
•1•1•21•2•Updated Aug 19, 2025Aug 19, 2025
pipeline-Nextflow-module
Public
Set of commonly used Nextflow modules
Nextflow
•
GNU General Public License v2.0
•0•0•9•1•Updated Aug 19, 2025Aug 19, 2025
pipeline-call-sSNV
Public
Nextflow pipeline to identify the somatic single nucleotide variants (sSNVs) by comparing a pair of tumor/normal samples.
pipeline
Nextflow
•
GNU General Public License v2.0
•2•6•36•3•Updated Aug 18, 2025Aug 18, 2025
tool-PlantUML-action
Public
Shell
•
GNU General Public License v2.0
•0•1•1•1•Updated Aug 18, 2025Aug 18, 2025
pipeline-align-DNA
Public
Nextflow pipeline to align paired DNA FASTQs and sort, mark duplicates, and index resulting alignment
pipeline
Nextflow
•
GNU General Public License v2.0
•1•4•25•2•Updated Aug 18, 2025Aug 18, 2025
pipeline-generate-SQC-BAM
Public
Nextflow pipeline to generate sample level QC data from BAM files
Groovy
•
GNU General Public License v2.0
•0•0•17•2•Updated Aug 18, 2025Aug 18, 2025
pipeline-calculate-mtDNA-CopyNumber
Public
Nextflow pipeline to calculate mitochondrial DNA copy number
Groovy
•
GNU General Public License v2.0
•0•0•0•0•Updated Aug 18, 2025Aug 18, 2025
pipeline-call-gSV
Public
Nextflow pipeline to call germline structural variants and copy number variants using DELLY and Manta
pipeline
R
•
GNU General Public License v2.0
•1•2•11•2•Updated Aug 18, 2025Aug 18, 2025
tool-NFTest
Public
CLI to automate Nextflow pipeline testing
Python
•
GNU General Public License v2.0
•1•12•16•1•Updated Aug 18, 2025Aug 18, 2025
tool-Nextflow-action
Public
Python
•
GNU General Public License v2.0
•0•0•7•2•Updated Aug 18, 2025Aug 18, 2025
pipeline-recalibrate-BAM
Public
Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration
Nextflow
•
GNU General Public License v2.0
•1•1•14•5•Updated Aug 15, 2025Aug 15, 2025
pipeline-call-sSV
Public
Nextflow pipeline to call somatic structural variants using DELLY, GRIDSS2 and Manta
pipeline
Nextflow
•
GNU General Public License v2.0
•0•2•17•2•Updated Aug 15, 2025Aug 15, 2025
pipeline-call-mtSNV
Public
Nextflow pipeline to detect mitochondrial SNV from normal or tumor BAMs or CRAMs: extracts and remaps mitochondorial reads then calls variants
pipeline nextflow
Nextflow
•
GNU General Public License v2.0
•0•1•18•3•Updated Aug 13, 2025Aug 13, 2025
tool-create-release
Public
GitHub reusable workflows to manage the release process
release-automation github-actions
Python
•
GNU General Public License v2.0
•0•0•0•0•Updated Aug 13, 2025Aug 13, 2025
metapipeline-DNA
Public
Nextflow pipeline to convert BAM to FASTQ, align, perform QC, assess targeted coverage, call gSNP, call sSNV, call mtSNV, call SVs, call sCNA, and perform subclonal reconstruction
pipeline
Groovy
•
GNU General Public License v2.0
•1•10•36•0•Updated Aug 13, 2025Aug 13, 2025
tool-Docker-action
Public
An Action to automatically build and push images to the GitHub Container registry. Includes automatic building of images for development.
docker cicd github-actions
JavaScript
•
GNU General Public License v2.0
•0•0•3•0•Updated Aug 13, 2025Aug 13, 2025
pipeline-calculate-targeted-coverage
Public
Nextflow pipeline to calculate read-depth related stats for targeted sequencing experiments
Nextflow
•
GNU General Public License v2.0
•0•0•10•2•Updated Aug 12, 2025Aug 12, 2025
package-moPepGen
Public
Multi-Omics Peptide Generator
genomics cancer-genomics proteomics proteogenomics neoantigen
Python
•
GNU General Public License v2.0
•4•23•27•1•Updated Aug 11, 2025Aug 11, 2025
pipeline-call-NonCanonicalPeptide
Public
Nextflow pipeline to generate custom databases of non-canonical peptides for proteogenomic analysis
Nextflow
•
GNU General Public License v2.0
•2•2•3•2•Updated Aug 11, 2025Aug 11, 2025
tool-static-analysis
Public
GitHub composite Action to perform static code analysis
Python
•
GNU General Public License v2.0
•0•0•1•0•Updated Aug 11, 2025Aug 11, 2025
package-CancerEvolutionVisualization
Public
Publication Quality Phylogenetic Tree Plots
R
•
GNU General Public License v2.0
•0•2•20•2•Updated Aug 11, 2025Aug 11, 2025
package-BoutrosLab-plotting-general
Public
Functions to Create Publication-Quality Plots
R
•4•15•61•2•Updated Aug 11, 2025Aug 11, 2025
package-ApplyPolygenicScore
Public
Utilities for matching a polygenic score coordinate file to a VCF input and the subsequent calculation of the provided polygenic score in each individual.
R
•
GNU General Public License v2.0
•0•0•8•0•Updated Aug 7, 2025Aug 7, 2025
docker-Delly
Public
Docker repository for Delly
Dockerfile
•
GNU General Public License v2.0
•0•0•0•0•Updated Jul 31, 2025Jul 31, 2025
docker-PLINK
Public
Dockerfile
•
GNU General Public License v2.0
•0•0•0•0•Updated Jul 25, 2025Jul 25, 2025
docker-BWA-MEM2
Public
Docker repository for BWA-MEM2 and SAMtools
docker
Dockerfile
•0•0•1•1•Updated Jul 25, 2025Jul 25, 2025
tool-SMCHet-scoring
Public
Automated scoring system for the SMC-Het Challenge
Python
•
Other
•0•1•0•0•Updated Jul 14, 2025Jul 14, 2025
Ligare
Public
Python
•
GNU General Public License v2.0
•0•1•16•2•Updated Jul 9, 2025Jul 9, 2025
package-iSubGen
Public
R
•
GNU General Public License v2.0
•0•1•4•1•Updated Jul 1, 2025Jul 1, 2025