SIMLR
This is the released version of SIMLR; for the devel version, see SIMLR.
Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)
Bioconductor version: Release (3.23)
Single-cell RNA-seq technologies enable high throughput gene expression measurement of individual cells, and allow the discovery of heterogeneity within cell populations. Measurement of cell-to-cell gene expression similarity is critical for the identification, visualization and analysis of cell populations. However, single-cell data introduce challenges to conventional measures of gene expression similarity because of the high level of noise, outliers and dropouts. We develop a novel similarity-learning framework, SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), which learns an appropriate distance metric from the data for dimension reduction, clustering and visualization.
Author: Daniele Ramazzotti [aut]
, Bo Wang [aut], Luca De Sano [cre, aut]
, Serafim Batzoglou [ctb]
Maintainer: Luca De Sano <luca.desano at gmail.com>
citation("SIMLR")):
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")
BiocManager::install("SIMLR")
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("SIMLR")| Introduction | HTML | R Script |
| Running SIMLR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, GeneExpression, ImmunoOncology, Sequencing, SingleCell, Software |
| Version | 1.38.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 years) |
| License | file LICENSE |
| Depends | R (>= 4.1.0) |
| Imports | parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy, RSpectra |
| System Requirements | |
| URL | https://github.com/BatzoglouLabSU/SIMLR |
| Bug Reports | https://github.com/BatzoglouLabSU/SIMLR |
See More
| Suggests | BiocGenerics, BiocStyle, testthat, knitr, igraph |
| Linking To | Rcpp |
| 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 | SIMLR_1.38.0.tar.gz |
| Windows Binary (x86_64) | SIMLR_1.38.0.zip |
| macOS Binary (big-sur-x86_64) | SIMLR_1.38.0.tgz |
| macOS Binary (sonoma-arm64) | SIMLR_1.38.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SIMLR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SIMLR |
| Bioc Package Browser | https://code.bioconductor.org/browse/SIMLR/ |
| Package Short Url | https://bioconductor.org/packages/SIMLR/ |
| Package Downloads Report | Download Stats |