Pinned Repositories
pluto-cwl
CWL workflows for helix filter scripts
IR-interpreter
Web app for clinical interpretation of Ion Reporter variant results
NGS580-nf
Target exome sequencing analysis for NYU NGS580 gene panel
Bioinformatics
Bioinformatics analysis scripts, workflows, general code examples
IGV-snapshot-automator
Script to automatically create and run IGV snapshot batchscripts
image-sort
Program to sort images by average color values
nextflow-demos
Example Nextflow pipelines and programming techniques
reference-annotations
Makefile for reference annotations for genes & genomic regions
reportIT
IonTorrent variant reporting pipeline for clinical interpretation of cancer panel results
stevekm's Repositories
stevekm/nf-dashboard-dj
Django web dashboard and API for Nextflow
stevekm/django-gunicorn-nginx
Django app deployment with Gunicorn and nginx
stevekm/slurm-cluster-vagrant
Vagrant setup for a slurm cluster
stevekm/Rx-Adherence-app
HCLS Hackathon project for tracking patient drug prescription usage
stevekm/slurm-cluster
Methods for building & deploying SLURM cluster from source code
stevekm/tmb-signatures-analysis
Tumor mutation burden & genomic signatures analysis workflow
stevekm/vep-annotation-nf
variant annotation workflow with VEP
stevekm/grep
GNU grep implemented in Rust
stevekm/newfile-detector-nf
Database-driven Nextflow app using Django ORM standalone
stevekm/entroPy
Add randomness to values
stevekm/fastq-bed-subset
Filter fastq file based on bed regions
stevekm/nextflow-ci
Unit test and CI implementation for Nextflow pipeline in Python
stevekm/BADAS_Nextflow_Tutorial
Nextflow tutorial for the BADAS series at NYU Center for Genomics and Systems Biology
stevekm/bwa-bench
stevekm/cut
GNU cut implemented in Rust
stevekm/demux-nf
Nextflow pipeline for Illumina NGS demultiplexing
stevekm/Django-Celery-Example
This is a simple example about how to create a progress bar in Django with Celery.
stevekm/fasta-counter
Count the number of nucleotides in .fasta entries
stevekm/IGV-snapshot-nf
Nextflow workflow for automated IGV snapshots
stevekm/IR-interpreter-flask
deprecated Flask version of IR-interpreter app
stevekm/lyz
Lab monitor program
stevekm/MuTect2_target_chunking
demo pipeline for testing different data chunking methods for MuTect2
stevekm/newfile-detector
App for detecting new files, using Django standalone ORM
stevekm/NGS580-demo-data
stevekm/patterns
A curated collections of Nextflow implementation patterns -- http://nextflow-io.github.io/patterns/index.html
stevekm/Pindel_target_chunking
stevekm/python-on-windows
Demo for setting up Python on Windows with conda
stevekm/rust-wasm-conda-demo
Demo setup of a Rust web assembly app in a conda environment
stevekm/snsxt
bioinformatics pipeline framework for data analysis
stevekm/tuco
Laboratory Information Management System (LIMS)