UCLA JCCC - Cancer Data Science

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69 repositories

pipeline-call-sSV
Public
Nextflow pipeline to call somatic structural variants using DELLY and Manta
pipeline
Groovy
•
GNU General Public License v2.0
•0•1•19•2•Updated Nov 5, 2024Nov 5, 2024
package-CancerEvolutionVisualization
Public
Publication Quality Phylogenetic Tree Plots
R
•
GNU General Public License v2.0
•0•2•25•6•Updated Nov 5, 2024Nov 5, 2024
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 Nov 5, 2024Nov 5, 2024
pipeline-call-sSNV
Public
A 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
•0•5•38•2•Updated Nov 4, 2024Nov 4, 2024
pipeline-call-gSNP
Public
Nextflow pipeline to call germline short variants using GATK
pipeline nextflow
Nextflow
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GNU General Public License v2.0
•1•1•21•2•Updated Nov 4, 2024Nov 4, 2024
pipeline-recalibrate-BAM
Public
Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration
Nextflow
•
GNU General Public License v2.0
•1•1•8•1•Updated Nov 4, 2024Nov 4, 2024
docker-Battenberg
Public
Docker repository for Wedge-lab/battenberg
Dockerfile
•
GNU General Public License v2.0
•0•0•4•2•Updated Nov 4, 2024Nov 4, 2024
Ligare
Public
Python
•
GNU General Public License v2.0
•0•0•12•0•Updated Nov 4, 2024Nov 4, 2024
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•1•Updated Nov 4, 2024Nov 4, 2024
pipeline-call-gSV
Public
Nextflow pipeline to call germline structural variants and copy number variants using DELLY and Manta
pipeline
Nextflow
•
GNU General Public License v2.0
•1•2•8•1•Updated Nov 4, 2024Nov 4, 2024
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•1•Updated Nov 4, 2024Nov 4, 2024
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•15•1•Updated Nov 1, 2024Nov 1, 2024
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 Nov 1, 2024Nov 1, 2024
project-method-AlgorithmEvaluation-BNCH-000082-SRCRNDSeed
Public
R
•
GNU General Public License v2.0
•0•1•20•0•Updated Nov 1, 2024Nov 1, 2024
prostate-cancer-m6a-paper
Public
Code for "The Landscape of N6-Methyladenosine in Localized Primary Prostate Cancer"
R
•0•0•0•0•Updated Nov 1, 2024Nov 1, 2024
docker-bam-readcount
Public
A utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions.
Dockerfile
•
GNU General Public License v2.0
•0•0•0•0•Updated Oct 31, 2024Oct 31, 2024
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
Nextflow
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GNU General Public License v2.0
•0•4•36•3•Updated Oct 31, 2024Oct 31, 2024
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•7•1•Updated Oct 31, 2024Oct 31, 2024
docker-MuSE
Public
Dockerfile
•
GNU General Public License v2.0
•0•0•2•0•Updated Oct 30, 2024Oct 30, 2024
pipeline-Nextflow-config
Public
Set of commonly used Nextflow configs
Groovy
•
GNU General Public License v2.0
•0•1•15•0•Updated Oct 28, 2024Oct 28, 2024
tool-Nextflow-action
Public
Python
•
GNU General Public License v2.0
•0•0•7•0•Updated Oct 28, 2024Oct 28, 2024
pipeline-Nextflow-module
Public
Set of commonly used Nextflow modules
Nextflow
•
GNU General Public License v2.0
•0•0•8•1•Updated Oct 28, 2024Oct 28, 2024
docker-BCFtools
Public
Dockerfile
•
GNU General Public License v2.0
•0•0•0•0•Updated Oct 28, 2024Oct 28, 2024
package-moPepGen
Public
Multi-Omics Peptide Generator
genomics cancer-genomics proteomics proteogenomics neoantigen
Python
•
GNU General Public License v2.0
•1•6•19•0•Updated Oct 25, 2024Oct 25, 2024
tool-static-analysis
Public
GitHub composite Action to perform static code analysis
Python
•
GNU General Public License v2.0
•0•0•0•0•Updated Oct 24, 2024Oct 24, 2024
tool-Docker-action
Public
docker cicd github-actions
JavaScript
•
GNU General Public License v2.0
•0•0•2•1•Updated Oct 18, 2024Oct 18, 2024
tool-PlantUML-action
Public
Shell
•
GNU General Public License v2.0
•0•1•1•3•Updated Oct 18, 2024Oct 18, 2024
package-PipeVal
Public
An easy to use CLI tool that can be used to validate different parameters in your NF script/pipeline.
Python
•
GNU General Public License v2.0
•1•5•15•4•Updated Oct 18, 2024Oct 18, 2024
tool-NFTest
Public
CLI to automate Nextflow pipeline testing
Python
•
GNU General Public License v2.0
•1•11•13•2•Updated Oct 18, 2024Oct 18, 2024
docker-Picard
Public
Docker repository for Picard
Dockerfile
•0•0•1•0•Updated Oct 14, 2024Oct 14, 2024