smartid
This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see smartid.
Scoring and Marker Selection Method Based on Modified TF-IDF
Bioconductor version: 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("smartid")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, Software, Transcriptomics |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (1 year) |
| 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 |
| 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 | smartid_1.2.0.tar.gz |
| Windows Binary (x86_64) | smartid_1.2.0.zip |
| macOS Binary (x86_64) | smartid_1.2.0.tgz |
| macOS Binary (arm64) | smartid_1.2.0.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 |