Repositories list

• Methylation

  Public
  DNA methylation for tumor subclassifications by methylation array.

  classifierrrmd

  R

  •1•3•1•0•Updated Dec 17, 2024Dec 17, 2024

• LG-PACT

  Public
  NYU Langone Genome PACT (Genome Profiling of Actionable Cancer Targets) targeted exome sequencing analysis pipeline.

  pythonhtmlmarkdown+ 6groovynextflowdocker-containermakefileslurmsingularity-container

  Nextflow

  •

  GNU General Public License v3.0

  •1•8•0•0•Updated Dec 13, 2024Dec 13, 2024

• demux-nf

  Public
  Nextflow pipeline for Illumina NGS demultiplexing

  demultiplexingbcl2fastqpipeline+ 1nextflow

  Nextflow

  •

  GNU General Public License v3.0

  •1•3•2•0•Updated Oct 21, 2024Oct 21, 2024

• tuco

  Public
  Laboratory Information Management System (LIMS)

  djangodatabaselims+ 1webapp

  Python

  •

  GNU General Public License v3.0

  •1•1•6•2•Updated Apr 21, 2023Apr 21, 2023

• onco-reporter

  Public
  Oncomine solid tumor reporting application

  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 1, 2023Mar 1, 2023

• automation-scripts

  Public
  repo for automation python/R scripts

  python-scriptiontorrentautomation

  Python

  •0•0•0•0•Updated Dec 9, 2022Dec 9, 2022

• heme-reporter

  Public
  Clinical reporting application for Oncomine Myeloid assay results.

  javascriptcsspython+ 5htmlnginxdjangojinja2conda

  HTML

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Jun 24, 2022Jun 24, 2022

• oncomine_automation

  Public
  oncomine automation

  MIT License

  •1•0•0•0•Updated May 27, 2022May 27, 2022

• NGS580-nf

  Public
  Target exome sequencing analysis for NYU NGS580 gene panel

  dockerexomeexome-sequencing-analysis+ 3pipelinenextflowsingularity

  Nextflow

  •

  GNU General Public License v3.0

  •5•10•17•0•Updated Sep 29, 2021Sep 29, 2021

• IR-interpreter

  Public
  Web app for clinical interpretation of Ion Reporter variant results

  djangowebappinterpretation+ 1ion-reporter

  Python

  •

  GNU General Public License v3.0

  •2•4•2•1•Updated Jun 10, 2021Jun 10, 2021

• excel2pdf-cov20

  Public
  JavaScript

  •0•1•0•0•Updated Apr 1, 2020Apr 1, 2020

• Validation_Writeup

  Public
  writeup of NYU LANGONE GENOME PACT pipeline

  HTML

  •0•0•0•0•Updated Nov 19, 2019Nov 19, 2019

• containers

  Public
  Docker and Singularity containers for Bioinformatics programs

  dockerbioinformaticscontainers+ 1singularity

  Dockerfile

  •

  GNU General Public License v3.0

  •2•3•0•0•Updated Oct 23, 2019Oct 23, 2019

• NGS580-demo-data

  Public
  Makefile

  •1•0•0•0•Updated Oct 14, 2019Oct 14, 2019

• lyz-nf

  Public
  lab monitoring program

  automationnextflow

  Nextflow

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Oct 13, 2019Oct 13, 2019

• util

  Public
  Utility modules for Python

  utilitybioinformaticsslurm+ 2pythonsge

  Python

  •

  GNU General Public License v3.0

  •2•6•0•0•Updated Sep 24, 2019Sep 24, 2019

• queue-stats

  Public
  Output stats on the SLURM HPC cluster

  slurmhpc-cluster

  Python

  •

  GNU General Public License v3.0

  •2•3•1•0•Updated Sep 16, 2019Sep 16, 2019

• IR-interpreter-flask

  Public
  deprecated Flask version of IR-interpreter app

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Mar 28, 2019Mar 28, 2019

• Methylation_QC

  Public
  Sample Quality Control for Illumina DNA methylation data

  1•0•0•0•Updated Nov 12, 2018Nov 12, 2018

• reportIT

  Public
  IonTorrent variant reporting pipeline for clinical interpretation of cancer panel results

  Python

  •

  GNU General Public License v3.0

  •4•0•0•0•Updated Oct 1, 2018Oct 1, 2018

• protocols

  Public
  Protocols for clinical analysis and managing lab data

  Python

  •1•0•0•0•Updated Aug 17, 2018Aug 17, 2018

• pmkb-cleaner

  Public
  Python

  •1•0•0•0•Updated Aug 1, 2018Aug 1, 2018

• snsxt

  Public
  bioinformatics pipeline framework for data analysis

  Python

  •

  GNU General Public License v3.0

  •3•4•17•0•Updated Apr 24, 2018Apr 24, 2018

• lyz

  Public
  Lab monitor program

  laboratoryautomationmonitoring+ 1lab

  Python

  •

  GNU General Public License v3.0

  •1•0•5•0•Updated Jan 29, 2018Jan 29, 2018

• sns_classes

  Public
  Python classes for the sns bioinformatics pipeline

  Python

  •0•0•1•0•Updated Nov 23, 2017Nov 23, 2017

• writeup

  Public
  writeup of NGS580 pipeline

  HTML

  •0•0•0•0•Updated Oct 17, 2017Oct 17, 2017

• sns

  Public
  illumina sequencing data analysis pipelines

  Shell

  •28•0•0•0•Updated Oct 10, 2017Oct 10, 2017

• sns_tasks

  Public
  Extra pipeline tasks to use with snsxt

  Python

  •0•0•0•0•Updated Aug 24, 2017Aug 24, 2017

• sns-wes-downstream-analysis

  Public
  R

  •0•0•0•0•Updated Jul 31, 2017Jul 31, 2017

• sns-wes-coverage-analysis

  Public
  A quick analysis of low coverage regions from the SNS Whole Exome Sequencing analysis pipeline output

  R

  •1•0•0•0•Updated Jul 20, 2017Jul 20, 2017