SETA
This is the development version of SETA; for the stable release version, see SETA.
All Bioconductor versions of SETA
3.24 (devel), 3.23 (release), 3.22
Single Cell Ecological Taxonomic Analysis
Bioconductor version: 3.24 · Package version: 1.3.0
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
From within R, enter citation("SETA"):
Kyle Kimler, Marc Elosua-Bayes. SETA: Single Cell Ecological Taxonomic Analysis. doi:10.18129/B9.bioc.SETA, R package version 1.3.0, https://bioconductor.org/packages/SETA.
Generated from the package metadata; it may differ from the package's own citation.
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.
Details
| Version | 1.3.0 |
| License | MIT + file LICENSE |
| URL | https://github.com/kkimler/SETA |
| Bug Reports | https://github.com/kkimler/SETA/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.22 (R-4.5) (less than a year) |
| Downloads rank | 2106 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataRepresentation, DimensionReduction, GeneExpression, Normalization, RNASeq, SingleCell, Software, StatisticalMethod, SystemsBiology, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/SETA/ |
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 |
Download
Follow the 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 (arm64) | SETA_1.3.0.tgz |
| macOS binary (x86_64) | 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 |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0)
Imports: dplyr, MASS, Matrix, SingleCellExperiment (>= 1.30.1), stats, tidygraph, rlang, utils
Suggests: BiocStyle, caret, glmnet, corrplot, ggplot2, ggraph, knitr, methods, patchwork, reshape2, rmarkdown, SeuratObject, Seurat, SummarizedExperiment, TabulaMurisSenisData, tidyr, tidytext, testthat (>= 3.0.0)