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@NYU-BFX Applied Bioinformatics Laboratories

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    28 repositories

    • 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 Jan 13, 2025Jan 13, 2025

    • hic-bench

      Public
      A set of pipelines for Hi-C and ChIP-Seq analysis.
      HTML
      •20•48•10•0•Updated Apr 11, 2024Apr 11, 2024

    • sns

      Public
      illumina sequencing data analysis pipelines
      Shell
      •
      MIT License
      •27•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
      •3•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
      •26•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
      •49•0•0•0•Updated Jan 4, 2018Jan 4, 2018

    • docker2singularity-demo

      Public
      A demo for converting Docker images to Singularity images.
      Makefile
      •34•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•25•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
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