smartid

This is the development version of smartid; for the stable release version, see smartid.

Scoring and Marker Selection Method Based on Modified TF-IDF


Bioconductor version: Development (3.20)

This package enables automated selection of group specific signature, especially for rare population. The package is developed for generating specifc lists of signature genes based on Term Frequency-Inverse Document Frequency (TF-IDF) modified methods. It can also be used as a new gene-set scoring method or data transformation method. Multiple visualization functions are implemented in this package.

Author: Jinjin Chen [aut, cre]

Maintainer: Jinjin Chen <chen.j at wehi.edu.au>

Citation (from within R, enter citation("smartid")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("smartid")

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("smartid")
smartid: Scoring and MARker selection method based on modified Tf-IDf HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneExpression, Software, Transcriptomics
Version 1.1.2
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.4)
Imports dplyr, ggplot2, graphics, Matrix, mclust, methods, mixtools, sparseMatrixStats, stats, SummarizedExperiment, tidyr, utils
System Requirements
URL https://davislaboratory.github.io/smartid
Bug Reports https://github.com/DavisLaboratory/smartid/issues
See More
Suggests BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater, splatter, testthat (>= 3.0.0), tidytext, UpSetR
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package smartid_1.1.2.tar.gz
Windows Binary smartid_1.1.2.zip (64-bit only)
macOS Binary (x86_64) smartid_1.1.2.tgz
macOS Binary (arm64) smartid_1.1.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/smartid
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/smartid
Bioc Package Browser https://code.bioconductor.org/browse/smartid/
Package Short Url https://bioconductor.org/packages/smartid/
Package Downloads Report Download Stats