UCLA JCCC - Cancer Data Science

All

70 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 Oct 19, 2024Oct 19, 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
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 Oct 18, 2024Oct 18, 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 Oct 18, 2024Oct 18, 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•14•3•Updated Oct 18, 2024Oct 18, 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•41•4•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
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•1•Updated Oct 18, 2024Oct 18, 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 Oct 18, 2024Oct 18, 2024
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 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
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 18, 2024Oct 18, 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
•
GNU General Public License v2.0
•0•4•36•3•Updated Oct 18, 2024Oct 18, 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 Oct 18, 2024Oct 18, 2024
package-CancerEvolutionVisualization
Public
Publication Quality Phylogenetic Tree Plots
R
•
GNU General Public License v2.0
•0•2•33•7•Updated Oct 18, 2024Oct 18, 2024
pipeline-Nextflow-module
Public
Set of commonly used Nextflow modules
Nextflow
•
GNU General Public License v2.0
•0•0•8•2•Updated Oct 17, 2024Oct 17, 2024
docker-BCFtools
Public
Dockerfile
•
GNU General Public License v2.0
•0•0•0•0•Updated Oct 17, 2024Oct 17, 2024
Ligare
Public
Python
•
GNU General Public License v2.0
•0•0•10•1•Updated Oct 17, 2024Oct 17, 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 Oct 14, 2024Oct 14, 2024
docker-Picard
Public
Docker repository for Picard
Dockerfile
•0•0•1•0•Updated Oct 14, 2024Oct 14, 2024
docker-MuSE
Public
Dockerfile
•
GNU General Public License v2.0
•0•0•3•1•Updated Oct 14, 2024Oct 14, 2024
docker-Delly
Public
Docker repository for Delly
Dockerfile
•
GNU General Public License v2.0
•0•0•1•0•Updated Oct 10, 2024Oct 10, 2024
package-BoutrosLab-plotting-general
Public
Functions to Create Publication-Quality Plots
R
•4•11•64•4•Updated Oct 10, 2024Oct 10, 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 1, 2024Oct 1, 2024
public-R-DigitalExercisePlatform
Public
Code for: A Digital, Decentralized Clinical Trial of Exercise Therapy in Cancer (DEXP)
R
•
GNU General Public License v2.0
•0•1•0•0•Updated Sep 24, 2024Sep 24, 2024
docker-SAMtools
Public
Dockerfile for samtools - a tools for "Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format".
docker
Dockerfile
•0•0•0•0•Updated Sep 18, 2024Sep 18, 2024
tool-R-CMD-check-action
Public
GitHub action for checking/testing R packages
R
•
GNU General Public License v2.0
•0•0•4•1•Updated Sep 17, 2024Sep 17, 2024
pipeline-call-NonCanonicalPeptide
Public
Nextflow pipeline to call non-canonical peptides as custom databases for proteogenomic analysis
Nextflow
•
GNU General Public License v2.0
•0•0•3•1•Updated Sep 9, 2024Sep 9, 2024
pipeline-Nextflow-config
Public
Set of commonly used Nextflow configs
Groovy
•
GNU General Public License v2.0
•0•1•15•0•Updated Sep 7, 2024Sep 7, 2024