CCR Collaborative Bioinformatics Resource

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83 repositories

ASPEN
Public
CCBR pipeline for preliminary QC, peak calling, differential chromatin accessibility analysis with ATACseq datasets 🌲
multiqc ngs-pipeline macs2 atac-seq-pipeline genrich
Shell
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MIT License
•0•0•17•0•Updated Feb 28, 2025Feb 28, 2025
CARLISLE
Public
Cut And Run Analysis Pipeline
workflow pipeline
Python
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MIT License
•4•4•15•1•Updated Feb 27, 2025Feb 27, 2025
MOSuite
Public
MultiOmicsSuite: R package for downstream multi-omics analysis
R
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Other
•0•2•22•0•Updated Feb 27, 2025Feb 27, 2025
CHAMPAGNE
Public
CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline
nextflow chip-seq
Nextflow
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MIT License
•2•0•59•1•Updated Feb 27, 2025Feb 27, 2025
SINCLAIR
Public
scRNASeq pipeline
HTML
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MIT License
•0•0•34•2•Updated Feb 26, 2025Feb 26, 2025
Tools
Public
Utilities for CCBR Bioinformatics Software 🛠️
Python
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MIT License
•4•1•8•0•Updated Feb 25, 2025Feb 25, 2025
LOGAN
Public
workflow bioinformatics pipeline
Nextflow
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MIT License
•4•1•21•0•Updated Feb 21, 2025Feb 21, 2025
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•3•10•2•Updated Feb 20, 2025Feb 20, 2025
actions
Public
🤖 GitHub Actions for CCBR repos
Python
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MIT License
•0•0•7•0•Updated Feb 18, 2025Feb 18, 2025
.github
Public
organizations readme
Python
•0•0•0•1•Updated Feb 16, 2025Feb 16, 2025
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 Feb 11, 2025Feb 11, 2025
nf-modules
Public
Reusable modules and subworkflows for CCBR nextflow pipelines
Nextflow
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MIT License
•0•0•10•3•Updated Feb 11, 2025Feb 11, 2025
RECAP
Public
RECAP for RE-CAlibration of P-values from ChIP-seq peak calling, by method of RE-sampling reads and re-CAlling Peaks.
Shell
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MIT License
•2•0•0•0•Updated Jan 22, 2025Jan 22, 2025
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•11•1•Updated Jan 21, 2025Jan 21, 2025
RENEE
Public
A comprehensive quality-control and quantification RNA-seq pipeline
Python
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MIT License
•4•4•14•0•Updated Jan 21, 2025Jan 21, 2025
CRISPIN
Public
CRISPR screen pipeline
Nextflow
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MIT License
•3•0•14•1•Updated Jan 21, 2025Jan 21, 2025
MAPLE
Public
Python
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MIT License
•1•0•0•0•Updated Jan 21, 2025Jan 21, 2025
TRANQUIL
Public
TRANQUIL (TRna AbundaNce QUantification pIpeLine)
Shell
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MIT License
•1•0•1•0•Updated Jan 21, 2025Jan 21, 2025
spacesavers2
Public
Python
•1•0•5•0•Updated Jan 21, 2025Jan 21, 2025
MAAPster
Public
MAAPster is a comprehensive tool to perform transcriptome analysis of human or mouse Affymetrix gene expression data
quality-control transcriptomics pathway-analysis differential-expression batch-correction microarray-data-analysis
R
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MIT License
•6•9•0•0•Updated Jan 21, 2025Jan 21, 2025
CCBR_circRNA_AmpliconSeq
Public
Snakemake workflow to process circRNA AmpliconSeq datasets generated to study circRNAs in KSHV and human hosts using divergent primers.
circrna amplicon-sequencing amplicon-pipeline circrna-pipeline snakemake-workflow
Shell
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MIT License
•1•0•0•0•Updated Jan 21, 2025Jan 21, 2025
ASCENT
Public
rMATs and IsoformSwitchAnalyeR workflow for multi-group multi-contrasts scenarios
Python
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MIT License
•2•0•2•0•Updated Jan 21, 2025Jan 21, 2025
CCBR1245_Ramaswami_nCounter
Public
R
•0•0•0•0•Updated Jan 14, 2025Jan 14, 2025
CCBR_tobias
Public
Tobias implementation for ATAC seq data.
Python
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MIT License
•1•1•2•1•Updated Jan 13, 2025Jan 13, 2025
Rodrigues-TLX3-MutIL7R-Leukemia
Public
Code for manuscript authored by Gisele Rodrigues in the Scott Durum lab
R
•0•0•0•0•Updated Jan 10, 2025Jan 10, 2025
CPTR-11-Beck-Canine-OsteoSarcoma-DSP-Analysis
Public
R
•1•0•0•0•Updated Jan 7, 2025Jan 7, 2025
DSP_Analysis
Public
A repository for general information and analysis templates for Nanostring's Digital Spatial Profiling
R
•1•0•0•0•Updated Jan 7, 2025Jan 7, 2025
TaskManagement
Public
Shell
•0•0•0•0•Updated Dec 30, 2024Dec 30, 2024
Dockers
Public
A collection of Dockerfiles to facilitate reproducibility across computing environments.
docker sbg singularity dnanexus biowulf
Dockerfile
•3•11•2•0•Updated Dec 3, 2024Dec 3, 2024
CCBR_NextflowTemplate
Public template
CCBR template for Nextflow workflows
nextflow templates techdev
Nextflow
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MIT License
•1•2•15•0•Updated Nov 25, 2024Nov 25, 2024