jvwong’s gists

jvwong / crossref_query.sh

Last active May 23, 2023 18:27

Crossref: Query

	QUERY="Inositol pyrophosphate dynamics reveals control of the yeast PHO starvation program through 1,5-IP8 and the SPX domain of Pho81"
	curl --get --data-urlencode "query.bibliographic=${QUERY}" "https://api.crossref.org/works/?filter=type:journal-article,type:posted-content&rows=1" \| jq '. \| { title: .message.items[0].title[0], abstract: .message.items[0].abstract, doi: .message.items[0].DOI, publisher: .message.items[0].publisher }'

jvwong / renew.sh

Created April 28, 2021 22:46

certbot certonly --webroot --webroot-path=<webroot path> --cert-name <certname> -d <domain> 

jvwong / parse_dotenv.bash

Created August 14, 2020 18:36 — forked from judy2k/parse_dotenv.bash

Parse a .env (dotenv) file directly using BASH

	# Pass the env-vars to MYCOMMAND
	eval $(egrep -v '^#' .env \| xargs) MYCOMMAND
	# … or ...
	# Export the vars in .env into your shell:
	export $(egrep -v '^#' .env \| xargs)

jvwong / feeds.xml

Created October 14, 2019 17:38 — forked from rossmounce/feeds.xml

My OPML bundle of academic journal RSS feeds related to my interests (phylogenetics, palaeontology), split into 4 different thematic sections.

	<?xml version="1.0" encoding="UTF-8"?>

	<opml version="1.0">
	<head>
	<title>Ross's academic journal RSS feed subscriptions</title>
	</head>
	<body>
	<outline text="General Biology Journals" title="General Biology Journals">
	<outline type="rss" text="BioEssays" title="BioEssays" xmlUrl="http://onlinelibrary.wiley.com/rss/journal/10.1002/(ISSN)1521-1878" htmlUrl="http://onlinelibrary.wiley.com/resolve/doi?DOI=10.1002%2F%28ISSN%291521-1878"/>
	<outline type="rss" text="Biol J Linn Soc" title="Biol J Linn Soc" xmlUrl="http://onlinelibrary.wiley.com/rss/journal/10.1111/(ISSN)1095-8312" htmlUrl="http://onlinelibrary.wiley.com/resolve/doi?DOI=10.1111%2F%28ISSN%291095-8312"/>

jvwong / cmd_line_opts.sh

Created June 7, 2019 17:05

Bash script for parsing cmd line args

jvwong / grep_row_table.sh

Last active January 21, 2020 15:07

	#!/bin/bash
	# Find row and print columns in tab-delimited file

	#tax_id GeneID PubMed_ID
	tax_id=9606
	GeneID=9518

	grep -Ei "^$tax_id\t$GeneID\t[0-9.]+$" ./data/gene2pubmed > result.txt

jvwong / faketimeout.js

Last active December 7, 2018 15:43

Promises and timers

	const TIMEOUT = 5000;

	const promiseTimeout = delay => new Promise( ( resolve, reject ) => setTimeout( () => reject( new Error('fake timeout') ), delay ) );


	const doSomethingAsync = ( ) => {
	return Promise.resolve()
	.then( () => promiseTimeout( TIMEOUT ) );
	};

jvwong / fishers.R

Created June 22, 2018 16:46

Fisher's exact for Miller et al.

	# Probability of GO term (GeneSet) in gene hits (Hits) from a screen

	# Initialize our relevant variables
	nBackground <- 407 # Total genes screened
	nGeneSet <- 18 # Genes in GO term that are in the bachground
	nHits <- 60 # Genes enriched in screen in background
	nOutsideGeneSet <- nBackground - nGeneSet # Genes not in GeneSet but in background
	nQueryPathway <- 0:nGeneSet # Overlap between query genes ('Hits') and GO term (in background)

	# Use the dhyper built-in function for hypergeometric probability

jvwong / enrichment.js

Created February 12, 2018 15:44

'enrichment' endpoint

	// const request = require('request');
	// const Promise = require('promise-simple');
	// const csv = require('csvtojson');
	// const fs = require('fs');
	// const _ = require('lodash');
	const enrichment = function (query) {

	var promise = new Promise(function(resolve, reject) {
	// do a thing, possibly async, then…

jvwong / gprofiler.js

Created February 6, 2018 21:09

Fetching from gProfiler

Jeffrey jvwong