iSEEhub
This is the released version of iSEEhub; for the devel version, see iSEEhub.
iSEE for the Bioconductor ExperimentHub
Bioconductor version: Release (3.23)
This package defines a custom landing page for an iSEE app interfacing with the Bioconductor ExperimentHub. The landing page allows users to browse the ExperimentHub, select a data set, download and cache it, and import it directly into a Bioconductor iSEE app.
Author: Kevin Rue-Albrecht [aut, cre]
Maintainer: Kevin Rue-Albrecht <kevinrue67 at gmail.com>
citation("iSEEhub")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("iSEEhub")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("iSEEhub")| Contributing to iSEEhub | HTML | R Script |
| Introduction to iSEEhub | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, ImmunoOncology Infrastructure, ShinyApps, SingleCell, Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | Artistic-2.0 |
| Depends | SummarizedExperiment, SingleCellExperiment, ExperimentHub |
| Imports | AnnotationHub, BiocManager, DT, iSEE, methods, rintrojs, S4Vectors, shiny, shinydashboard, shinyjs, utils |
| System Requirements | |
| URL | https://github.com/iSEE/iSEEhub |
| Bug Reports | https://support.bioconductor.org/t/iSEEhub |
See More
| Suggests | BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), nullrangesData |
| Linking To | |
| Enhances | BioPlex, biscuiteerData, bodymapRat, CLLmethylation, CopyNeutralIMA, curatedAdipoArray, curatedAdipoChIP, curatedMetagenomicData, curatedTCGAData, DMRcatedata, DuoClustering2018, easierData, emtdata, epimutacionsData, FieldEffectCrc, GenomicDistributionsData, GSE103322, GSE13015, GSE62944, HDCytoData, HMP16SData, HumanAffyData, imcdatasets, mcsurvdata, MetaGxBreast, MetaGxOvarian, MetaGxPancreas, MethylSeqData, muscData, NxtIRFdata, ObMiTi, quantiseqr, restfulSEData, RLHub, sesameData, SimBenchData, SingleCellMultiModal, SingleMoleculeFootprintingData, spatialDmelxsim, STexampleData, TabulaMurisData, TabulaMurisSenisData, TENxVisiumData, tissueTreg, VectraPolarisData, xcoredata |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | iSEEhub_1.14.0.tar.gz |
| Windows Binary (x86_64) | iSEEhub_1.14.0.zip |
| macOS Binary (big-sur-x86_64) | iSEEhub_1.14.0.tgz |
| macOS Binary (sonoma-arm64) | iSEEhub_1.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/iSEEhub |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/iSEEhub |
| Bioc Package Browser | https://code.bioconductor.org/browse/iSEEhub/ |
| Package Short Url | https://bioconductor.org/packages/iSEEhub/ |
| Package Downloads Report | Download Stats |