Applied Bioinformatics Laboratories's repositories
lncRNA-screen
lncRNA-screen
UCSC-custom-track-generator
Script to automatically generate custom tracks to load on UCSC
AutoReportLite
Automatic analysis pipline & reporting template
hic-bench-demo
Demo dataset & usage for HiC-Bench ChIP-Seq pipeline
hic-bench_documentation
User manuals for the HiC-Bench software
nf-bio-basic
Nextflow basic Bioinformatics workflow for testing and demonstration
reference-annotations
Makefile for reference annotations for hg19 genes & genomic regions
TCGA_downloads
How to download TCGA data from GDC portal
annotate-peaks
Scripts for .bed file genomic region annotation with various tools
conda-phoenix
how to set up Anaconda and Conda environments on NYULMC phoenix HPC cluster
containers
Docker and Singularity containers for Bioinformatics programs
docker-sge
Dockerfile to build a container with SGE installed
docker2singularity-demo
A demo for converting Docker images to Singularity images.
IGV-snapshot-automator
Script to automatically create and run IGV snapshot batchscripts
neoantigen-pipeline
Call somatic mutations and call Class 1 and 2 epitopes
nextflow-boilerplate
Boilerplate code for Nextflow pipelines
nextflow-demos
Example Nextflow pipelines and programming techniques
peak-type-summary
ChIPSeeker genomic region summary plotting and annotation script
peaks-report
A quick report to make a plot & table of the number of peaks per BED file in a dir
singularity-samtools-demo
Singularity container for samtools