UCLA JCCC - Cancer Data Science

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73 repositories

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•22•4•Updated Dec 28, 2024Dec 28, 2024
package-iSubGen
Public
R
•
GNU General Public License v2.0
•0•1•4•0•Updated Dec 27, 2024Dec 27, 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•6•0•Updated Dec 26, 2024Dec 26, 2024
pipeline-recalibrate-BAM
Public
Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration
Nextflow
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GNU General Public License v2.0
•1•1•9•1•Updated Dec 20, 2024Dec 20, 2024
Ligare
Public
Python
•
GNU General Public License v2.0
•0•0•17•2•Updated Dec 19, 2024Dec 19, 2024
pipeline-call-sSNV
Public
Nextflow pipeline to identify the somatic single nucleotide variants (sSNVs) by comparing a pair of tumor/normal samples.
pipeline
Nextflow
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GNU General Public License v2.0
•0•5•33•2•Updated Dec 18, 2024Dec 18, 2024
pipeline-Nextflow-config
Public
Set of commonly used Nextflow configs
Groovy
•
GNU General Public License v2.0
•0•1•16•1•Updated Dec 17, 2024Dec 17, 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 Dec 17, 2024Dec 17, 2024
package-CancerEvolutionVisualization
Public
Publication Quality Phylogenetic Tree Plots
R
•
GNU General Public License v2.0
•0•2•18•4•Updated Dec 16, 2024Dec 16, 2024
pipeline-call-sSV
Public
Nextflow pipeline to call somatic structural variants using DELLY and Manta
pipeline
Groovy
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GNU General Public License v2.0
•0•2•17•2•Updated Dec 16, 2024Dec 16, 2024
pipeline-align-DNA
Public
Nextflow pipeline to align paired DNA FASTQs and sort, mark duplicates, and index resulting alignment
pipeline
Nextflow
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GNU General Public License v2.0
•1•4•25•1•Updated Dec 16, 2024Dec 16, 2024
pipeline-call-gSV
Public
Nextflow pipeline to call germline structural variants and copy number variants using DELLY and Manta
pipeline
Nextflow
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GNU General Public License v2.0
•1•2•10•2•Updated Dec 16, 2024Dec 16, 2024
pipeline-calculate-targeted-coverage
Public
Nextflow pipeline to calculate read-depth related stats for targeted sequencing experiments
Nextflow
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GNU General Public License v2.0
•0•0•10•1•Updated Dec 16, 2024Dec 16, 2024
pipeline-generate-SQC-BAM
Public
Nextflow pipeline to generate sample level QC data from BAM files
Groovy
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GNU General Public License v2.0
•0•0•15•1•Updated Dec 16, 2024Dec 16, 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
Groovy
•
GNU General Public License v2.0
•0•4•36•0•Updated Dec 16, 2024Dec 16, 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•16•5•Updated Dec 14, 2024Dec 14, 2024
project-CancerBiology-OutlierAnalysis
Public
R
•
GNU General Public License v2.0
•0•1•0•0•Updated Dec 13, 2024Dec 13, 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 Dec 3, 2024Dec 3, 2024
megalinter
Public
🦙 MegaLinter analyzes 50 languages, 22 formats, 21 tooling formats, excessive copy-pastes, spelling mistakes and security issues in your repository sources with a GitHub Action, other CI tools or locally.
Dockerfile
•
GNU Affero General Public License v3.0
•242•0•0•0•Updated Nov 26, 2024Nov 26, 2024
package-VennDiagram
Public
Generate High-Resolution Venn and Euler Plots
R
•
GNU General Public License v2.0
•1•2•6•1•Updated Nov 20, 2024Nov 20, 2024
tool-NFTest
Public
CLI to automate Nextflow pipeline testing
Python
•
GNU General Public License v2.0
•1•11•13•0•Updated Nov 19, 2024Nov 19, 2024
package-OutSeekR
Public
R
•
GNU General Public License v2.0
•0•0•2•0•Updated Nov 15, 2024Nov 15, 2024
pipeline-call-NonCanonicalPeptide
Public
Nextflow pipeline to call non-canonical peptides as custom databases for proteogenomic analysis
Nextflow
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GNU General Public License v2.0
•1•0•3•1•Updated Nov 15, 2024Nov 15, 2024
docker-Battenberg
Public
Docker repository for Wedge-lab/battenberg
Dockerfile
•
GNU General Public License v2.0
•0•0•5•1•Updated Nov 14, 2024Nov 14, 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
docker-MuSE
Public
Dockerfile
•
GNU General Public License v2.0
•0•0•2•0•Updated Oct 30, 2024Oct 30, 2024
tool-Nextflow-action
Public
Python
•
GNU General Public License v2.0
•0•0•7•0•Updated Oct 28, 2024Oct 28, 2024