Repositories list

• pipeline-atac2hic

  Public
  Pipeline to predict HiC matrices from ATAC-seq fastq files using maxATAC and C.Origami

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 21, 2024Dec 21, 2024

• hic-bench

  Public
  A set of pipelines for Hi-C and ChIP-Seq analysis.

  HTML

  •20•44•10•0•Updated Apr 11, 2024Apr 11, 2024

• sns

  Public
  illumina sequencing data analysis pipelines

  Shell

  •

  MIT License

  •28•1•0•0•Updated Sep 23, 2022Sep 23, 2022

• neoantigen-pipeline

  Public
  Call somatic mutations and call Class 1 and 2 epitopes

  Python

  •0•0•0•0•Updated Jun 2, 2021Jun 2, 2021

• TCGA_downloads

  Public
  How to download TCGA data from GDC portal

  R

  •1•2•0•1•Updated May 3, 2021May 3, 2021

• Gene_fusion

  Public
  0•0•0•0•Updated Mar 30, 2021Mar 30, 2021

• computational-tools

  Public
  0•0•0•0•Updated Apr 13, 2020Apr 13, 2020

• deep-drug-response

  Public
  R

  •

  GNU General Public License v3.0

  •10•1•0•0•Updated Apr 18, 2019Apr 18, 2019

• containers

  Public
  Docker and Singularity containers for Bioinformatics programs

  Dockerfile

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated Oct 18, 2018Oct 18, 2018

• nf-bio-basic

  Public
  Nextflow basic Bioinformatics workflow for testing and demonstration

  Makefile

  •18•1•0•0•Updated Sep 6, 2018Sep 6, 2018

• RNA-Seq_Standard

  Public
  Python

  •12•11•1•0•Updated Aug 3, 2018Aug 3, 2018

• nextflow-demos

  Public
  Example Nextflow pipelines and programming techniques

  Nextflow

  •

  GNU General Public License v3.0

  •25•0•0•0•Updated May 31, 2018May 31, 2018

• nextflow-boilerplate

  Public
  Boilerplate code for Nextflow pipelines

  Nextflow

  •1•0•0•0•Updated May 8, 2018May 8, 2018

• conda-phoenix

  Public
  how to set up Anaconda and Conda environments on NYULMC phoenix HPC cluster

  Makefile

  •1•0•0•0•Updated Jan 17, 2018Jan 17, 2018

• IGV-snapshot-automator

  Public
  Script to automatically create and run IGV snapshot batchscripts

  Python

  •50•0•0•0•Updated Jan 4, 2018Jan 4, 2018

• docker2singularity-demo

  Public
  A demo for converting Docker images to Singularity images.

  Makefile

  •36•0•0•0•Updated Jan 4, 2018Jan 4, 2018

• reference-annotations

  Public
  Makefile for reference annotations for hg19 genes & genomic regions

  Makefile

  •4•1•0•0•Updated Dec 22, 2017Dec 22, 2017

• docker-sge

  Public
  Dockerfile to build a container with SGE installed

  Shell

  •18•0•0•0•Updated Dec 8, 2017Dec 8, 2017

• singularity-samtools-demo

  Public
  Singularity container for samtools

  Shell

  •1•0•0•0•Updated Dec 6, 2017Dec 6, 2017

• annotate-peaks

  Public
  Scripts for .bed file genomic region annotation with various tools

  R

  •1•0•0•0•Updated Oct 11, 2017Oct 11, 2017

• peak-type-summary

  Public
  ChIPSeeker genomic region summary plotting and annotation script

  R

  •1•0•0•0•Updated Oct 10, 2017Oct 10, 2017

• hic-bench-demo

  Public
  Demo dataset & usage for HiC-Bench ChIP-Seq pipeline

  Shell

  •1•1•0•0•Updated Oct 9, 2017Oct 9, 2017

• peaks-report

  Public
  A quick report to make a plot & table of the number of peaks per BED file in a dir

  R

  •3•0•0•0•Updated Oct 9, 2017Oct 9, 2017

• lncRNA-screen

  Public
  lncRNA-screen

  Shell

  •16•26•1•0•Updated Apr 19, 2017Apr 19, 2017

• UCSC-custom-track-generator

  Public
  Script to automatically generate custom tracks to load on UCSC

  Python

  •3•2•0•0•Updated Apr 6, 2017Apr 6, 2017

• AutoReportLite

  Public
  Automatic analysis pipline & reporting template

  TeX

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Sep 27, 2016Sep 27, 2016

• g-content

  Public
  Gene content in n-grams, lateral gene transfer detection

  0•0•0•0•Updated Aug 23, 2016Aug 23, 2016

• hic-bench_documentation

  Public
  User manuals for the HiC-Bench software

  TeX

  •4•1•0•0•Updated Apr 7, 2016Apr 7, 2016