SETA
This is the development version of SETA; for the stable release version, see SETA.
Single Cell Ecological Taxonomic Analysis
Bioconductor version: Development (3.24)
Tools for compositional and other sample-level ecological analyses and visualizations tailored for single-cell RNA-seq data. SETA includes functions for taxonomizing celltypes, normalizing data, performing statistical tests, and visualizing results. Several tutorials are included to guide users and introduce them to key concepts. SETA is meant to teach users about statistical concepts underlying ecological analysis methods so they can apply them to their own single-cell data.
Author: Kyle Kimler [aut, cre]
, Marc Elosua-Bayes [aut]
Maintainer: Kyle Kimler <kkimler at broadinstitute.org>
citation("SETA")):
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("SETA")
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("SETA")| Comparing samples with SETA | HTML | R Script |
| Introduction to SETA ecological transforms and sample-level latent spaces | HTML | R Script |
| Multi-Resolution Compositional Analysis in scRNA-seq: Reference Frames with SETA | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataRepresentation, DimensionReduction, GeneExpression, Normalization, RNASeq, SingleCell, Software, StatisticalMethod, SystemsBiology, Transcriptomics, Visualization |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | dplyr, MASS, Matrix, SingleCellExperiment(>= 1.30.1), stats, tidygraph, rlang, utils |
| System Requirements | |
| URL | https://github.com/kkimler/SETA |
| Bug Reports | https://github.com/kkimler/SETA/issues |
See More
| Suggests | BiocStyle, caret, glmnet, corrplot, ggplot2, ggraph, knitr, methods, patchwork, reshape2, rmarkdown, SeuratObject, Seurat, SummarizedExperiment, TabulaMurisSenisData, tidyr, tidytext, 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 | SETA_1.3.0.tar.gz |
| Windows Binary (x86_64) | SETA_1.3.0.zip |
| macOS Binary (big-sur-x86_64) | SETA_1.3.0.tgz |
| macOS Binary (sonoma-arm64) | SETA_1.3.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SETA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SETA |
| Bioc Package Browser | https://code.bioconductor.org/browse/SETA/ |
| Package Short Url | https://bioconductor.org/packages/SETA/ |
| Package Downloads Report | Download Stats |