sparrow

DOI:10.18129/B9.bioc.sparrow

This is thedevelopmentversion of sparrow; for the stable release version, seesparrow.

Take command of set enrichment analyses through a unified interface

Bioconductor version: Development (3.16)

Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package.

Author: Steve Lianoglou [aut, cre], Arkadiusz Gladki [ctb], Denali Therapeutics [fnd] (2018+), Genentech [fnd] (2014 - 2017)

Maintainer: Steve Lianoglou

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("sparrow")

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("sparrow")

HTML	R Script	Performing gene set enrichment analyses with sparrow
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneSetEnrichment,Pathways,Software
Version	1.3.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
License	MIT + fileLICENSE
Depends	R (>= 4.0)
Imports	babelgene(>= 21.4),BiocGenerics,BiocParallel,BiocSet,checkmate,circlize,ComplexHeatmap(>= 2.0),data.table(>= 1.10.4),DelayedMatrixStats,edgeR(>= 3.18.1),ggplot2(>= 2.2.0), graphics, grDevices,GSEABase,irlba,limma,Matrix, methods,plotly(>= 4.9.0), stats, utils,viridis
LinkingTo
Suggests	AnnotationDbi,BiasedUrn,Biobase(>= 2.24.0),BiocStyle,DESeq2,dplyr,dtplyr,fgsea,GSVA,GO.db,goseq,hexbin,magrittr,matrixStats,msigdbr(>= 7.4.1),KernSmooth,knitr,PANTHER.db(>= 1.0.3),R.utils,reactome.db,rmarkdown,SummarizedExperiment,statmod,stringr,testthat,webshot
SystemRequirements
Enhances
URL	https://github.com/lianos/sparrow
BugReports	https://github.com/lianos/sparrow/issues
Depends On Me
Imports Me
Suggests Me	gCrisprTools
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	sparrow_1.3.0.tar.gz
Windows Binary	sparrow_1.3.0.zip
macOS 10.13 (High Sierra)	sparrow_1.3.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/sparrow
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/sparrow
Package Short Url	//www.andersvercelli.com/packages/sparrow/
Package Downloads Report	Download Stats