Package: corral 1.15.0

Lauren Hsu

corral: Correspondence Analysis for Single Cell Data

Correspondence analysis (CA) is a matrix factorization method, and is similar to principal components analysis (PCA). Whereas PCA is designed for application to continuous, approximately normally distributed data, CA is appropriate for non-negative, count-based data that are in the same additive scale. The corral package implements CA for dimensionality reduction of a single matrix of single-cell data, as well as a multi-table adaptation of CA that leverages data-optimized scaling to align data generated from different sequencing platforms by projecting into a shared latent space. corral utilizes sparse matrices and a fast implementation of SVD, and can be called directly on Bioconductor objects (e.g., SingleCellExperiment) for easy pipeline integration. The package also includes additional options, including variations of CA to address overdispersion in count data (e.g., Freeman-Tukey chi-squared residual), as well as the option to apply CA-style processing to continuous data (e.g., proteomic TOF intensities) with the Hellinger distance adaptation of CA.

Authors:Lauren Hsu [aut, cre], Aedin Culhane [aut]

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Peer review:

On BioConductor:corral-1.15.0(bioc 3.20)corral-1.14.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

25 exports 0.71 score 77 dependencies

Last updated 2 months agofrom:9b176e9234

Exports:add_embeddings2scelistall_arebiplot_corralcompsvdcorralcorral_matcorral_preproccorral_scecorralmcorralm_matlistcorralm_sceearthmover_distget_pct_var_exp_svdget_weightslist2matna2zeropairwise_rvplot_embeddingplot_embedding_scervscal_varscal_var_matsce2matlisttrim_matdistvar_stabilize

Dependencies:abindaskpassBiobaseBiocBaseUtilsBiocGenericsclicolorspacecpp11crayoncurldata.tableDelayedArraydichromatdplyrfansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggthemesgluegridExtragtablehttrIRangesirlbaisobandjsonlitelabelinglatticelifecyclemagrittrmapprojmapsMASSMatrixMatrixGenericsmatrixStatsmgcvmimeMultiAssayExperimentmunsellnlmeopensslpalspillarpkgconfigplyrpurrrR6RColorBrewerRcppRcppEigenreshape2rlangS4ArraysS4VectorsscalesSingleCellExperimentSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttransportUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc