CCR Collaborative Bioinformatics Resource

Dockers

A collection of Dockerfiles to facilitate reproducibility across computing environments.

CARLISLE

Cut And Run Analysis Pipeline

METRO

Mouse nEoanTigen pRedictOr

CCBR_SnakemakeTemplate

Barebones framework for creating new snakemake workflows.

RENEE

A comprehensive quality-control and quantification RNA-seq pipeline

CCBR_NextflowTemplate

CCBR template for Nextflow workflows

CHARLIE

Circrnas in Host And viRuses anaLysis pIpEline for Detection Annotation Quantification of circRNAs

LOGAN

reneeTools

R helper functions for RENEE

Tools

Tools created by CCBR/NCBR members

XAVIER

An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH

.github

organizations readme

ASPEN

CCBR pipeline for preliminary QC and peak calling from ATACseq datasets

bioinfo-pf-curie-chip-seq

Nextflow pipeline for ChIP-seq data quality controls and analysis

ccbr1238

CCBR1245_Ramaswami_nCounter

CCBR_tobias

Tobias implementation for ATAC seq data.

CHAMPAGNE

CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline

chromVAR

chromatin Variability Across Regions (of the genome!)

CPTR-9-Weigert-DSP-Analysis

CPTR_5_DSP_Krug

CRISPIN

CRISPR screen pipeline

DSP_Analysis

A repository for general information and analysis templates for Nanostring's Digital Spatial Profiling

l2p

List to pathway, or l2p, is an R package for gene set enrichment analysis that is optimized for speed.

nf-modules

Reusable modules and subworkflows for CCBR nextflow pipelines

nf-sandbox

a repo for testing and toying with nextflow

nfcore_methylseq

nf-core Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

parkit

Park folders or tarballs into HPCDME

spacesavers2

TRANQUIL

TRANQUIL (TRna AbundaNce QUantification pIpeLine)