scPassport
This is the released version of scPassport; for the devel version, see scPassport.
Passport System for Single-Cell Objects
Bioconductor version: Release (3.23)
Stamps Seurat, SingleCellExperiment, and SummarizedExperiment objects with a persistent metadata passport. For Seurat objects the passport is stored in the misc slot; for SingleCellExperiment and SummarizedExperiment objects it is stored in the metadata slot. Tracks animal info, experiment details, lineage (parent/child relationships), RDS registry numbers, processing logs, and custom fields. Includes an interactive Shiny gadget to fill and update the passport, and a read mode to print the full passport to console. The passport persists inside the RDS file with no external files needed.
Author: Sedat Kacar [aut, cre]
Maintainer: Sedat Kacar <sedatkacar56 at gmail.com>
citation("scPassport")):
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("scPassport")
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("scPassport")| Getting Started with scPassport | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, Infrastructure, SingleCell, Software, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.3) |
| Imports | shiny, miniUI, Rcpp, S4Vectors |
| System Requirements | |
| URL | https://github.com/sedatkacar56/scPassport |
| Bug Reports | https://github.com/sedatkacar56/scPassport/issues |
See More
| Suggests | Seurat, SingleCellExperiment, SummarizedExperiment, knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | Rcpp |
| 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 | scPassport_1.0.0.tar.gz |
| Windows Binary (x86_64) | scPassport_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | scPassport_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | scPassport_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scPassport |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scPassport |
| Bioc Package Browser | https://code.bioconductor.org/browse/scPassport/ |
| Package Short Url | https://bioconductor.org/packages/scPassport/ |
| Package Downloads Report | Download Stats |