iSEEfier
This is the released version of iSEEfier; for the devel version, see iSEEfier.
Streamlining the creation of initial states for starting an iSEE instance
Bioconductor version: Release (3.23)
iSEEfier provides a set of functionality to quickly and intuitively create, inspect, and combine initial configuration objects. These can be conveniently passed in a straightforward manner to the function call to launch iSEE() with the specified configuration. This package currently works seamlessly with the sets of panels provided by the iSEE and iSEEu packages, but can be extended to accommodate the usage of any custom panel (e.g. from iSEEde, iSEEpathways, or any panel developed independently by the user).
Author: Najla Abassi [aut, cre]
, Federico Marini [aut]
Maintainer: Najla Abassi <abassi.nejla96 at gmail.com>
citation("iSEEfier")):
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("iSEEfier")
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("iSEEfier")| iSEEfier_userguide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, Clustering, DimensionReduction, FeatureExtraction, GUI, GeneExpression, ImmunoOncology, ShinyApps, SingleCell, Software, Transcription, Transcriptomics, Visualization |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1.0) |
| Imports | iSEE, iSEEu, methods, ggplot2, igraph, rlang, stats, SummarizedExperiment, SingleCellExperiment, visNetwork, BiocBaseUtils |
| System Requirements | |
| URL | https://github.com/NajlaAbassi/iSEEfier |
| Bug Reports | https://github.com/NajlaAbassi/iSEEfier/issues |
See More
| Suggests | knitr, rmarkdown, scater, scRNAseq, org.Mm.eg.db, scuttle, BiocStyle, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| 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 | iSEEfier_1.8.0.tar.gz |
| Windows Binary (x86_64) | iSEEfier_1.8.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | iSEEfier_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | iSEEfier_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/iSEEfier |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/iSEEfier |
| Bioc Package Browser | https://code.bioconductor.org/browse/iSEEfier/ |
| Package Short Url | https://bioconductor.org/packages/iSEEfier/ |
| Package Downloads Report | Download Stats |