dce

DOI:10.18129/B9.bioc.dce

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, seedce.

Pathway Enrichment Based on Differential Causal Effects

Bioconductor version: 3.14

Compute differential causal effects (dce) on (biological) networks. Given observational samples from a control experiment and non-control (e.g., cancer) for two genes A and B, we can compute differential causal effects with a (generalized) linear regression. If the causal effect of gene A on gene B in the control samples is different from the causal effect in the non-control samples the dce will differ from zero. We regularize the dce computation by the inclusion of prior network information from pathway databases such as KEGG.

Author: Kim Philipp Jablonski [aut, cre], Martin Pirkl [aut]

Maintainer: Kim Philipp Jablonski

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("dce")

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

查看文档的版本包age installed in your system, start R and enter:

browseVignettes("dce")

HTML	R Script	Get started
HTML	R Script	Overview of pathway network databases
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression,GeneExpression,GraphAndNetwork,KEGG,Network,NetworkEnrichment,Regression,Software,StatisticalMethod
Version	1.2.0
In Bioconductor since	BioC 3.13 (R-4.1) (1 year)
License	GPL-3
Depends	R (>= 4.1)
Imports	stats, methods,assertthat,graph,pcalg,purrr,tidyverse,Matrix,ggraph,tidygraph,ggplot2,rlang,expm,MASS,CombinePValue,edgeR,epiNEM,igraph,metap,mnem,naturalsort,ppcor,glm2,graphite,reshape2,dplyr,glue,Rgraphviz,harmonicmeanp,org.Hs.eg.db,logger
LinkingTo
Suggests	knitr,rmarkdown,testthat(>= 2.1.0),BiocStyle,formatR,cowplot,dagitty,lmtest,sandwich,devtools,curatedTCGAData,TCGAutils,SummarizedExperiment
SystemRequirements
Enhances
URL	https://github.com/cbg-ethz/dce
BugReports	https://github.com/cbg-ethz/dce/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	dce_1.2.0.tar.gz
Windows Binary	dce_1.2.0.zip
macOS 10.13 (High Sierra)	dce_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/dce
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/dce
Package Short Url	//www.andersvercelli.com/packages/dce/
Package Downloads Report	Download Stats