scConform
This is the development version of scConform; to use it, please install the devel version of Bioconductor.
Conformal Inference for Cell Type Annotation
Bioconductor version: Development (3.23)
Builds prediction interval for cell type annotation using conformal inference and conformal risk control. It provides two main methods. The first one gives prediction intervals with coverage guarantees based on standard conformal inference. The second one instead gives hierarchical prediction intervals that are consistent with the cell ontology.
Author: Daniela Corbetta [aut, cre]
, Tram Nguyen [ctb], Nitesh Turaga [ctb], Ludwig Geistlinger [ctb]
Maintainer: Daniela Corbetta <daniela.corbetta at unipd.it>
citation("scConform")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("scConform")
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("scConform")| Conformal Prediction for cell type annotation | HTML | R Script |
| Reference Manual |
Details
| biocViews | Annotation, Classification, SingleCell, Software |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | Artistic-2.0 |
| Depends | R (>= 4.6.0) |
| Imports | igraph, stats, SummarizedExperiment, BiocParallel, Rgraphviz |
| System Requirements | |
| URL | https://github.com/ccb-hms/scConform |
| Bug Reports | https://github.com/ccb-hms/scConform/issues |
See More
| Suggests | knitr, Matrix, rmarkdown, BiocStyle, VGAM, ontoProc, MerfishData, doParallel, scuttle, SingleCellExperiment, scran, 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 | scConform_0.99.4.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/scConform |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scConform |
| Bioc Package Browser | https://code.bioconductor.org/browse/scConform/ |
| Package Short Url | https://bioconductor.org/packages/scConform/ |
| Package Downloads Report | Download Stats |