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automation-scripts

repo for automation python/R scripts

containers

Docker and Singularity containers for Bioinformatics programs

demultiplexing-stats

Demultiplexing stats report designed for NextSeq output

demux-nf

Nextflow pipeline for Illumina NGS demultiplexing

excel2pdf-cov20

heme-reporter

Clinical reporting application for Oncomine Myeloid assay results.

ir-interpreter

Web app for clinical interpretation of Ion Reporter variant results

ir-interpreter-flask

deprecated Flask version of IR-interpreter app

lg-pact

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

lyz

Lab monitor program

lyz-nf

lab monitoring program

methylation

DNA methylation for tumor subclassifications by methylation array.

methylation_qc

Sample Quality Control for Illumina DNA methylation data

ngs580-demo-data

ngs580-nf

Target exome sequencing analysis for NYU NGS580 gene panel

onco-reporter

Oncomine solid tumor reporting application

oncomine_automation

oncomine automation

pmkb-cleaner

protocols

Protocols for clinical analysis and managing lab data

queue-stats

Output stats on the SLURM HPC cluster

reportit

IonTorrent variant reporting pipeline for clinical interpretation of cancer panel results

sns

illumina sequencing data analysis pipelines

sns-wes-coverage-analysis

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

sns-wes-downstream-analysis

sns_classes

Python classes for the sns bioinformatics pipeline

sns_tasks

Extra pipeline tasks to use with snsxt

snsxt

bioinformatics pipeline framework for data analysis

tuco

Laboratory Information Management System (LIMS)

util

Utility modules for Python

validation_writeup

writeup of NYU LANGONE GENOME PACT pipeline