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 (3.24)
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")):
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")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, Software, Transcriptomics |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| 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), tibble, 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_1.9.0.tar.gz |
| Windows Binary (x86_64) | smartid_1.9.0.zip |
| macOS Binary (big-sur-x86_64) | smartid_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | smartid_1.9.0.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 |