CCR Collaborative Bioinformatics Resource

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81 repositories

actions
Public
🤖 GitHub Actions for CCBR repos
Python
•
MIT License
•0•0•5•0•Updated Nov 8, 2024Nov 8, 2024
nf-sandbox
Public
a repo for testing and toying with nextflow & gh actions
Python
•
MIT License
•0•0•3•0•Updated Nov 7, 2024Nov 7, 2024
CCBR_NextflowTemplate
Public template
CCBR template for Nextflow workflows
nextflow templates techdev
Nextflow
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MIT License
•1•2•9•0•Updated Nov 7, 2024Nov 7, 2024
CCBR_tobias
Public
Tobias implementation for ATAC seq data.
Python
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MIT License
•1•1•2•0•Updated Nov 7, 2024Nov 7, 2024
RENEE
Public
A comprehensive quality-control and quantification RNA-seq pipeline
Python
•
MIT License
•4•3•16•0•Updated Nov 7, 2024Nov 7, 2024
ASPEN
Public
CCBR pipeline for preliminary QC and peak calling from ATACseq datasets 🌲
multiqc ngs-pipeline macs2 atac-seq-pipeline genrich
Shell
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MIT License
•2•0•4•0•Updated Nov 7, 2024Nov 7, 2024
CHARLIE
Public
Circrnas in Host And viRuses anaLysis pIpEline for Detection Annotation Quantification of circRNAs
circrna ngs-analysis ngs-pipeline circularrna-detection
Python
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MIT License
•1•2•14•1•Updated Nov 6, 2024Nov 6, 2024
MOSuite
Public
MultiOmicsSuite: R package for downstream multi-omics analysis
R
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Other
•0•1•30•0•Updated Nov 5, 2024Nov 5, 2024
XAVIER
Public
An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH
Python
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MIT License
•3•1•7•0•Updated Nov 5, 2024Nov 5, 2024
Dockers
Public
A collection of Dockerfiles to facilitate reproducibility across computing environments.
docker singularity biowulf sbg dnanexus
Dockerfile
•3•11•2•0•Updated Nov 5, 2024Nov 5, 2024
DSP_Analysis
Public
A repository for general information and analysis templates for Nanostring's Digital Spatial Profiling
R
•0•0•2•0•Updated Nov 5, 2024Nov 5, 2024
LOGAN
Public
workflow bioinformatics pipeline
Nextflow
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MIT License
•4•1•18•0•Updated Nov 4, 2024Nov 4, 2024
Tools
Public
Utilities for CCBR Bioinformatics Software ⚒️
Python
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MIT License
•4•1•9•0•Updated Nov 4, 2024Nov 4, 2024
.github
Public
organizations readme
Python
•0•0•0•0•Updated Nov 3, 2024Nov 3, 2024
CPTR-12-Wang-DSP-Analysis
Public
R
•0•0•0•0•Updated Oct 31, 2024Oct 31, 2024
HowTos
Public
How To Guides on various data management and other CCBR-related tasks.
1•0•2•0•Updated Oct 30, 2024Oct 30, 2024
parkit
Public
Park folders or tarballs into HPCDME 🚙
Python
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MIT License
•0•0•2•0•Updated Oct 30, 2024Oct 30, 2024
CPTR-11-Beck-Canine-OsteoSarcoma-DSP-Analysis
Public
R
•0•0•0•0•Updated Oct 18, 2024Oct 18, 2024
CRISPIN
Public
CRISPR screen pipeline
Nextflow
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MIT License
•3•0•12•1•Updated Oct 16, 2024Oct 16, 2024
CARLISLE
Public
Cut And Run Analysis Pipeline
workflow pipeline
Python
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MIT License
•4•4•12•0•Updated Oct 14, 2024Oct 14, 2024
CPTR-10-Tosato-Mouse-WTA-DSP-Analysis
Public
R
•0•0•0•0•Updated Oct 8, 2024Oct 8, 2024
CHAMPAGNE
Public
CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline
nextflow chip-seq
Nextflow
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MIT License
•2•0•51•0•Updated Oct 1, 2024Oct 1, 2024
spacesavers2
Public
Python
•1•0•4•0•Updated Oct 1, 2024Oct 1, 2024
l2ptest
Public
l2p testing
C
•0•0•0•0•Updated Aug 30, 2024Aug 30, 2024
l2p
Public
List to pathway, or l2p, is an R package for gene set enrichment analysis that is optimized for speed.
c r-package functional-enrichment-analysis over-representation-analysis l2p
C
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MIT License
•2•0•0•0•Updated Aug 23, 2024Aug 23, 2024
CCBR_SnakemakeTemplate
Public template
Barebones framework for creating new snakemake workflows.
snakemake templates techdev
Shell
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MIT License
•1•3•1•0•Updated Aug 20, 2024Aug 20, 2024
build-renee-refs
Public
Build genome references for RENEE
Python
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MIT License
•0•0•0•0•Updated Aug 6, 2024Aug 6, 2024
CCBR1245_Ramaswami_nCounter
Public
R
•0•0•0•0•Updated Aug 5, 2024Aug 5, 2024
CPTR_5_DSP_Krug
Public
HTML
•1•0•0•0•Updated Jul 31, 2024Jul 31, 2024
CPTR-9-Weigert-DSP-Analysis
Public
HTML
•1•0•0•0•Updated Jul 24, 2024Jul 24, 2024