scECODA
This is the released version of scECODA; for the devel version, see scECODA.
Single-Cell Exploratory Compositional Data Analysis
Bioconductor version: Release (3.23)
The scECODA R package provides a complete workflow for the analysis and visualization of compositional data, primarily focusing on cell type proportions derived from single-cell data. It implements specialized methods, such as the Centered Log-Ratio (CLR) transformation, to properly analyze proportional data while avoiding the biases introduced by the compositional constraint. The package encapsulates data management, transformation, and analysis into a single SummarizedExperiment object, offering downstream tools for dimensionality reduction via PCA, calculating critical metrics like the Adjusted Rand Index (ARI) and Modularity to quantify sample grouping quality, and generating high-quality visualizations like heatmaps and scatter plots.
Author: Christian Halter [aut, cre]
, Massimo Andreatta [aut]
, Santiago Carmona [aut]
, Swiss Cancer Research Foundation [fnd]
Maintainer: Christian Halter <scecoda.dev at gmail.com>
citation("scECODA")):
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("scECODA")
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("scECODA")| scECODA.html | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, Clustering, DimensionReduction, FeatureExtraction, Normalization, Preprocessing, PrincipalComponent, SingleCell, Software, Transcriptomics, Visualization |
| Version | 1.0.1 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | BiocGenerics, cluster, corrplot, DESeq2, dplyr, factoextra (>= 2.0.0), ggplot2, ggpubr, ggrepel, gtools, Matrix, mclust, methods, pheatmap, plotly, rlang, rstatix, S4Vectors, stringr, SummarizedExperiment(>= 1.34.0), tidyr, vegan |
| System Requirements | |
| URL | https://github.com/carmonalab/scECODA |
| Bug Reports | https://github.com/carmonalab/scECODA/issues |
See More
| Suggests | Seurat (>= 5.0.0), igraph, knitr, rmarkdown, BiocStyle, testthat, scRNAseq |
| 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 | scECODA_1.0.1.tar.gz |
| Windows Binary (x86_64) | scECODA_1.0.1.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | scECODA_1.0.1.tgz |
| macOS Binary (sonoma-arm64) | scECODA_1.0.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scECODA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scECODA |
| Bioc Package Browser | https://code.bioconductor.org/browse/scECODA/ |
| Package Short Url | https://bioconductor.org/packages/scECODA/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |