Sean Davis seandavi

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├── DESCRIPTION <<<--- This is the only file needed to have an R package!
├── NAMESPACE
├── R
│   └── hello.R
...
└── man
 └── hello.Rd

	---
	title: "Big Data Approaches"
	subtitle: "Where to go with Bioconductor"
	event: "Bioconductor Technical Advisory Board Meeting"
	#author: Sean Davis
	date: "`r Sys.Date()`"
	output:
	BiocStyle::html_document
	---

	library(tibble)
	library(jsonlite)
	library(curl)
	as_tibble(jsonlite::fromJSON(curl('https://api.omicidx.cancerdatasci.org/sra/studies/ERP009142/runs?size=500'))$hits)

	"""
	Creates, updates, and deletes a job object.
	"""

	from os import path
	import os

	import yaml
	import uuid

	from elasticsearch import Elasticsearch
	cli = Elasticsearch() # may need to create

	from elasticsearch_dsl import connections
	connections.add_connection('default',cli.client)

	import elasticsearch_dsl as dsl
	class Study(dsl.Document):
	class Index:
	name = 'sra_study-zq'

	class Main {
	public static void main(String[] args) {
	String s1 = "Taylor Swift";
	String s2 = "John Boyega";
	String s3 = "Emma Stone";
	String s4 = s1.substring(2,s1.length()-3).toLowerCase();
	String s5 = s2.substring(2,s2.length()-3).toLowerCase();
	String s6 = s3.substring(2,s3.length()-3).toLowerCase();
	System.out.println(s1 + ">>>" + s4 + "\n" + s2 + ">>>" + s5 + "\n"+ s3 + ">>>" + s6);
	}

	# To accompany: https://seandavi.github.io/2019/05/single-cell-packages-and-dependencies-in-bioconductor-using-biocpkgtools/
	library(BiocPkgTools)
	library(igraph)
	library(visNetwork)
	bpl = biocPkgList()
	bpl_sc = bpl[grepl('SingleCell', bpl$biocViews),]
	dep_df = buildPkgDependencyDataFrame()
	dep_graph = buildPkgDependencyIgraph(dep_df)
	dep_graph_sc = inducedSubgraphByPkgs(dep_graph, bpl_sc$Package )
	ledges <- data.frame(color = c("green", "lightblue", "red"),