Package: countland 0.1.2

countland: Analysis of Biological Count Data, Especially from Single-Cell RNA-Seq

A set of functions for applying a restricted linear algebra to the analysis of count-based data. See the accompanying preprint manuscript: "Normalizing need not be the norm: count-based math for analyzing single-cell data" Church et al (2022) <doi:10.1101/2022.06.01.494334> This tool is specifically designed to analyze count matrices from single cell RNA sequencing assays. The tools implement several count-based approaches for standard steps in single-cell RNA-seq analysis, including scoring genes and cells, comparing cells and clustering, calculating differential gene expression, and several methods for rank reduction. There are many opportunities for further optimization that may prove useful in the analysis of other data. We provide the source code freely available at <https://github.com/shchurch/countland> and encourage users and developers to fork the code for their own purposes.

Authors:Church Samuel H. [aut, cre]

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NEWS

Peer review:

Bug tracker:https://github.com/shchurch/countland/issues

On CRAN:

20 exports 0.09 score 28 dependencies 21 scripts 211 downloads

Last updated 8 months agofrom:348e6886f6. Checks:OK: 7. Indexed: yes.

Exports:ClustercountlandDotEmbedPlotEigengapPlotEmbeddingPlotGeneCountsPlotIMAPlotIMAElbowPlotMarkerPlotSharedCountsRankMarkerGenesRestoreCountsRunIMAScoreCellsScoreGenesSharedCountsSubsampleSubsetCellsSubsetGenes

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr