Applied Bioinformatics Laboratories

New York, NY

Pinned Repositories

AutoReportLite
Automatic analysis pipline & reporting template
Language:TeX1 4 00
deep-drug-response
Language:R1 5 00
hic-bench
A set of pipelines for Hi-C and ChIP-Seq analysis.
Language:HTML45 15 1620
hic-bench_documentation
User manuals for the HiC-Bench software
Language:TeX1 5 04
lncRNA-screen
lncRNA-screen
Language:Shell26 5 116
nf-bio-basic
Nextflow basic Bioinformatics workflow for testing and demonstration
Language:Makefile1 4 00
reference-annotations
Makefile for reference annotations for hg19 genes & genomic regions
Language:Makefile1 4 00
RNA-Seq_Standard
Language:Python11 12 212
TCGA_downloads
How to download TCGA data from GDC portal
Language:R2 5 01
UCSC-custom-track-generator
Script to automatically generate custom tracks to load on UCSC
Language:Python2 4 00

Applied Bioinformatics Laboratories's Repositories

NYU-BFX/hic-bench
A set of pipelines for Hi-C and ChIP-Seq analysis.
Language:HTML45 15 1620
NYU-BFX/lncRNA-screen
lncRNA-screen
Language:Shell26 5 116
NYU-BFX/RNA-Seq_Standard
Language:Python11 12 212
NYU-BFX/TCGA_downloads
How to download TCGA data from GDC portal
Language:R2 5 01
NYU-BFX/UCSC-custom-track-generator
Script to automatically generate custom tracks to load on UCSC
Language:Python2 4 00
NYU-BFX/AutoReportLite
Automatic analysis pipline & reporting template
Language:TeX1 4 00
NYU-BFX/deep-drug-response
Language:R1 5 00
NYU-BFX/hic-bench-demo
Demo dataset & usage for HiC-Bench ChIP-Seq pipeline
Language:Shell1 4 00
NYU-BFX/hic-bench_documentation
User manuals for the HiC-Bench software
Language:TeX1 5 04
NYU-BFX/nf-bio-basic
Nextflow basic Bioinformatics workflow for testing and demonstration
Language:Makefile1 4 00
NYU-BFX/reference-annotations
Makefile for reference annotations for hg19 genes & genomic regions
Language:Makefile1 4 00
NYU-BFX/sns
illumina sequencing data analysis pipelines
Language:Shell1 4 01
NYU-BFX/annotate-peaks
Scripts for .bed file genomic region annotation with various tools
Language:R4 0
NYU-BFX/computational-tools
4 0
NYU-BFX/conda-phoenix
how to set up Anaconda and Conda environments on NYULMC phoenix HPC cluster
Language:Makefile4 0
NYU-BFX/containers
Docker and Singularity containers for Bioinformatics programs
Language:Dockerfile4 0
NYU-BFX/docker-sge
Dockerfile to build a container with SGE installed
Language:Shell4 0
NYU-BFX/docker2singularity-demo
A demo for converting Docker images to Singularity images.
Language:Makefile4 0
NYU-BFX/g-content
Gene content in n-grams, lateral gene transfer detection
3 0
NYU-BFX/Gene_fusion
5 0
NYU-BFX/IGV-snapshot-automator
Script to automatically create and run IGV snapshot batchscripts
Language:Python4 0
NYU-BFX/neoantigen-pipeline
Call somatic mutations and call Class 1 and 2 epitopes
Language:Python5 0
NYU-BFX/nextflow-boilerplate
Boilerplate code for Nextflow pipelines
Language:Nextflow4 0
NYU-BFX/nextflow-demos
Example Nextflow pipelines and programming techniques
Language:Nextflow4 0
NYU-BFX/peak-type-summary
ChIPSeeker genomic region summary plotting and annotation script
Language:R4 0
NYU-BFX/peaks-report
A quick report to make a plot & table of the number of peaks per BED file in a dir
Language:R4 0
NYU-BFX/pipeline-atac2hic
Pipeline to predict HiC matrices from ATAC-seq fastq files using maxATAC and C.Origami
Language:Python
NYU-BFX/singularity-samtools-demo
Singularity container for samtools
Language:Shell4 0