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3-nextflow-patterns

This repo contains code snippets and markdown illustrating 5 useful Nextflow patterns.

awesome_malaria_parasite_imaging_datasets

This repository is an attempt to list all malaria parasite imaging datasets (blood smears). Contributions welcome!

badas_nextflow_tutorial

Nextflow tutorial for the BADAS series at NYU Center for Genomics and Systems Biology

bioconda-recipes-phosphodisco

Conda recipes for the bioconda channel.

bokeh_genome_explorer

This is my first Bokeh server app. I built it to help me visualize some underlying properties of bacterial genomes.

cel-seq-pipeline

configs

Config files used to define parameters specific to compute environments at different Institutions.

covid19

UNDER CONSTRUCTION: A pipeline for the analysis of COVID-19 pandemic data.

dask-tutorial

Dask tutorial

dask_tutorial2

Short Dask Tutorial for my local Coding Club

deus-excel-machina

When you are sent a spreadsheet that has been filled in without automated processing in mind, processing and cleaning can become daunting. This is a quick tutorial with an example spreadsheet teaching you some common techniques.

filterblade-public-assets

Contains public custom files, such as extra hover descriptions for items listed on FilterBlade.

folium_tutorial

A short folium tutorial that I created based on Rob Story's talk "Up and Down the Python Data and Web Visualization". I use public data from NYC's opendata portal as well as publicly maintained geoJSON files.

golub_dataset_class_prediction_python

This repository contains a Jupyter Notebook with a couple classifiers trained on the famous Golub_dataset

gro_aggregator

Biotech event aggregator web page source code; #django

gro_your_career_2019_rsvp_analysis

In this repo, I am analyzing the RSVP data gathered for the GRO Your Career Conference 2019: http://groyourcareer2019.splashthat.com

itp_spring_2020

nextflow_parse_issue

nextflow_patterns

This is a collection of nextflow snippets I have created for myself for when I couldn't find something on http://nextflow-io.github.io/patterns/ or needed to clarify a pattern for myself.

nyubiotechsite

website for the NYU Biotech Association

singularity_containers

SingularityHub container definition for a containers that I need for my workflows that aren't already available on biocontainers etc.

vim_settings

A repo for my .vimrc, filetype.vim, syntax, etc.

website

Nextflow public web site