NYU-Molecular-Pathology

Pinned Repositories

containers
Docker and Singularity containers for Bioinformatics programs
Language:Dockerfile3 4 03
demux-nf
Nextflow pipeline for Illumina NGS demultiplexing
Language:Nextflow3 3 102
heme-reporter
Clinical reporting application for Oncomine Myeloid assay results.
Language:HTML10
IR-interpreter
Web app for clinical interpretation of Ion Reporter variant results
Language:Python4 3 112
LG-PACT
NYU Langone Genome PACT (Genome Profiling of Actionable Cancer Targets) targeted exome sequencing analysis pipeline.
Language:Nextflow8 3 01
Methylation
DNA methylation for tumor subclassifications by methylation array.
Language:R3 3 11
NGS580-nf
Target exome sequencing analysis for NYU NGS580 gene panel
Language:Nextflow10 3 436
queue-stats
Output stats on the SLURM HPC cluster
Language:Python3 3 22
snsxt
bioinformatics pipeline framework for data analysis
Language:Python4 3 363
util
Utility modules for Python
Language:Python6 3 02

NYU-Molecular-Pathology's Repositories

NYU-Molecular-Pathology/NGS580-nf
Target exome sequencing analysis for NYU NGS580 gene panel
Language:Nextflow10 3 436
NYU-Molecular-Pathology/LG-PACT
NYU Langone Genome PACT (Genome Profiling of Actionable Cancer Targets) targeted exome sequencing analysis pipeline.
Language:Nextflow8 3 01
NYU-Molecular-Pathology/util
Utility modules for Python
Language:Python6 3 02
NYU-Molecular-Pathology/IR-interpreter
Web app for clinical interpretation of Ion Reporter variant results
Language:Python4 3 112
NYU-Molecular-Pathology/snsxt
bioinformatics pipeline framework for data analysis
Language:Python4 3 363
NYU-Molecular-Pathology/containers
Docker and Singularity containers for Bioinformatics programs
Language:Dockerfile3 4 03
NYU-Molecular-Pathology/demux-nf
Nextflow pipeline for Illumina NGS demultiplexing
Language:Nextflow3 3 102
NYU-Molecular-Pathology/Methylation
DNA methylation for tumor subclassifications by methylation array.
Language:R3 3 11
NYU-Molecular-Pathology/queue-stats
Output stats on the SLURM HPC cluster
Language:Python3 3 22
NYU-Molecular-Pathology/excel2pdf-cov20
Language:JavaScript1 3 00
NYU-Molecular-Pathology/heme-reporter
Clinical reporting application for Oncomine Myeloid assay results.
Language:HTML10
NYU-Molecular-Pathology/lyz-nf
lab monitoring program
Language:Nextflow1 2 01
NYU-Molecular-Pathology/tuco
Laboratory Information Management System (LIMS)
Language:Python1 3 61
NYU-Molecular-Pathology/automation-scripts
repo for automation python/R scripts
Language:Python0 4 00
NYU-Molecular-Pathology/IR-interpreter-flask
deprecated Flask version of IR-interpreter app
Language:Python3 01
NYU-Molecular-Pathology/lyz
Lab monitor program
Language:Python3 51
NYU-Molecular-Pathology/Methylation_QC
Sample Quality Control for Illumina DNA methylation data
2 01
NYU-Molecular-Pathology/NGS580-demo-data
Language:Makefile2 01
NYU-Molecular-Pathology/onco-reporter
Oncomine solid tumor reporting application
Language:HTML
NYU-Molecular-Pathology/oncomine_automation
oncomine automation
1
NYU-Molecular-Pathology/pmkb-cleaner
Language:Python3 0
NYU-Molecular-Pathology/protocols
Protocols for clinical analysis and managing lab data
Language:Python2 01
NYU-Molecular-Pathology/reportIT
IonTorrent variant reporting pipeline for clinical interpretation of cancer panel results
Language:Python2 0
NYU-Molecular-Pathology/sns
illumina sequencing data analysis pipelines
Language:Shell3 0
NYU-Molecular-Pathology/sns-wes-coverage-analysis
A quick analysis of low coverage regions from the SNS Whole Exome Sequencing analysis pipeline output
Language:R3 0
NYU-Molecular-Pathology/sns-wes-downstream-analysis
Language:R2 0
NYU-Molecular-Pathology/sns_classes
Python classes for the sns bioinformatics pipeline
Language:Python2 1
NYU-Molecular-Pathology/sns_tasks
Extra pipeline tasks to use with snsxt
Language:Python2 0
NYU-Molecular-Pathology/Validation_Writeup
writeup of NYU LANGONE GENOME PACT pipeline
Language:HTML2 0
NYU-Molecular-Pathology/writeup
writeup of NGS580 pipeline
Language:HTML2 0