Kozo Nishida kozo2

pywikipathways and py4cytoscape

by Kozo Nishida, Barry Demchak, Alexander Pico

pywikipathways 0.0.2
py4cytoscape 0.0.10

WikiPathways is a well-known repository for biological pathways that provides unique tools to the research community for content creation, editing and utilization [@Pico2008].

Python is a powerful programming language and environment for statistical and exploratory data analysis.

この記事はWorkflow Advent Calendar 2020の4日目の記事です。 4日に分けてSnakemake Tutorialを和訳します。これはその4日のうちの第2日目です。

Basics: An example workflow

Please make sure that you have activated the environment we created before, and that you have an open terminal in the working directory you have created. 以前に作成した環境をアクティブ化したこと、加えて作成した作業ディレクトリでターミナルを開いていることを確認してください。

A Snakemake workflow is defined by specifying rules in a Snakefile. Rules decompose the workflow into small steps (e.g., the application of a single tool) by specifying how to create sets of output files from sets of input files.

Introduction to Bioconductor Annotation Resources

Bioc 2020: 29-31 July

Instructors

James W. MacDonald ([email protected])
Lori Shepherd ([email protected])

Create A Package (パッケージを作る)

A package is a collection of functions that work together in a cohesive manner to achieve a goal. It (should) include detailed documentation through man pages and vignettes and (should) be tested for accuracy and efficiency. Writing R extensions is a very detailed manual provided by CRAN that explains writing packages and what the structure of a package should look like. This vignette is going to walk you through making your first package in RStudio as well as how to submitt a package to Bioconductor.

I replaced devtools::install_github to BiocManager::install.

	addAllostericEdges <- function(allostericEdges, networkSUID,
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	targetlayer = "kegg_global"){

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	allostericTable = read.table(allostericEdges)

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	<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
	<properties>
	<cytoscape.api.version>3.6.0</cytoscape.api.version>

	<maven-compiler-plugin.version>3.6.1</maven-compiler-plugin.version>
	<maven-bundle-plugin.version>5.1.1</maven-bundle-plugin.version>

	<osgi.api.version>4.2.0</osgi.api.version>

	KEGG_GLOBAL_PATHWAY_IDS <- c("01100", "01110", "01120", "01200", "01210",
	"01212", "01230", "01220")

	importLayer <- function(networkFilePath){
	fileExtension <- tools::file_ext(networkFilePath)
	if (fileExtension %in% c("sif", "gml", "xgmml", "xml")){
	message("Importing ", networkFilePath)
	suID <- RCy3::importNetworkFromFile(file = paste(getwd(), "/",
	networkFilePath, sep=""))
	Sys.sleep(3)

	File path File name Title MS1 count MSMS count PRECURSORMZ PRECURSORTYPE Structure rank 1 Total score Databases Formula Ontology InChIKey SMILES Structure rank 2 Total score Databases Formula Ontology InChIKey SMILES Structure rank 3 Total score Databases Formula Ontology InChIKey SMILES Structure rank 4 Total score Databases Formula Ontology InChIKey SMILES Structure rank 5 Total score Databases Formula Ontology InChIKey SMILES Structure rank 6 Total score Databases Formula Ontology InChIKey SMILES Structure rank 7 Total score Databases Formula Ontology InChIKey SMILES Structure rank 8 Total score Databases Formula Ontology InChIKey SMILES Structure rank 9 Total score Databases Formula Ontology InChIKey SMILES Structure rank 10 Total score Databases Formula Ontology InChIKey SMILES
	C:\Users\knishida\Desktop\MS-FINDER demo files\S-propylmercaptoglutathione.mat S-propylmercaptoglutathione Unknown 18 36 382.1105 [M+H]+
	C:\Users\knishida\Des