NYU-Molecular-Pathology

NYU-Molecular-Pathology's repositories

NGS580-nf

Target exome sequencing analysis for NYU NGS580 gene panel

Language:NextflowGPL-3.010 3 43

LG-PACT

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

Language:NextflowGPL-3.08 30

util

Utility modules for Python

Language:PythonGPL-3.06 30

IR-interpreter

Web app for clinical interpretation of Ion Reporter variant results

Language:PythonGPL-3.04 3 11

snsxt

bioinformatics pipeline framework for data analysis

Language:PythonGPL-3.04 3 36

containers

Docker and Singularity containers for Bioinformatics programs

Language:DockerfileGPL-3.03 30

demux-nf

Nextflow pipeline for Illumina NGS demultiplexing

Language:NextflowGPL-3.03 3 10

Methylation

DNA methylation for tumor subclassifications by methylation array.

Language:R3 3 1

queue-stats

Output stats on the SLURM HPC cluster

Language:PythonGPL-3.03 3 2

excel2pdf-cov20

Language:JavaScript1 30

heme-reporter

Clinical reporting application for Oncomine Myeloid assay results.

Language:HTMLGPL-3.0100

lyz-nf

lab monitoring program

Language:NextflowGPL-3.01 20

tuco

Laboratory Information Management System (LIMS)

Language:PythonGPL-3.01 3 6

automation-scripts

repo for automation python/R scripts

Language:Python030

IR-interpreter-flask

deprecated Flask version of IR-interpreter app

Language:PythonGPL-3.0030

lyz

Lab monitor program

Language:PythonGPL-3.003 5

Methylation_QC

Sample Quality Control for Illumina DNA methylation data

020

NGS580-demo-data

Language:Makefile020

onco-reporter

Oncomine solid tumor reporting application

Language:HTMLGPL-3.0000

oncomine_automation

oncomine automation

MIT000

pmkb-cleaner

Language:Python030

protocols

Protocols for clinical analysis and managing lab data

Language:Python020

reportIT

IonTorrent variant reporting pipeline for clinical interpretation of cancer panel results

Language:PythonGPL-3.0020

sns

illumina sequencing data analysis pipelines

Language:Shell030

sns-wes-coverage-analysis

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

Language:R030

sns-wes-downstream-analysis

Language:R020

sns_classes

Python classes for the sns bioinformatics pipeline

Language:Python02 1

sns_tasks

Extra pipeline tasks to use with snsxt

Language:Python020

Validation_Writeup

writeup of NYU LANGONE GENOME PACT pipeline

Language:HTML020

writeup

writeup of NGS580 pipeline

Language:HTML020