apbCatalogR
This is the development version of apbCatalogR; to use it, please install the devel version of Bioconductor.
Look Up APB Result Fields by Meaning
Bioconductor version: Development (3.24)
Looks up the fields of AnnData Proteomics Bridge (APB) results by meaning, such as a PEP or an unnormalized intensity, without naming vendor columns. Reimplements the apb-catalog API on the bundle apb-catalog releases: reviewed sets, apb2's rule levels and expected answers. Reads APB results, as h5ad, Parquet or DuckDB, into anndataR objects.
Author: Witold E. Wolski [aut] 
, Witek Wolski [cre] , Functional Genomics Center Zurich [fnd]
Maintainer: Witek Wolski <wewolski at gmail.com>
citation("apbCatalogR")):Witold E. Wolski. apbCatalogR: Look Up APB Result Fields by Meaning. doi:10.18129/B9.bioc.apbCatalogR, R package version 0.99.4, https://bioconductor.org/packages/apbCatalogR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("apbCatalogR")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("apbCatalogR")| Looking up APB fields by meaning | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, MassSpectrometry, Proteomics, Software |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | anndataR (>= 1.2.2), jsonlite, Matrix, R6, stats, tools, utils |
| System Requirements | |
| URL | https://anndata-omics-bridge.github.io/apbCatalogR/ https://github.com/anndata-omics-bridge/apbCatalogR |
| Bug Reports | https://github.com/anndata-omics-bridge/apbCatalogR/issues |
See More
| Suggests | altdoc, arrow, BiocStyle, covr, cyclocomp, DBI, devtools, duckdb, knitr, lintr, rcmdcheck, rhdf5, rmarkdown, roxygen2, testthat (>= 3.0.0), withr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/apbCatalogR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/apbCatalogR |
| Package Short Url | https://bioconductor.org/packages/apbCatalogR/ |
| Package Downloads Report | Download Stats |