ggtreeExtra - An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"
'ggtreeExtra' extends the method for mapping and visualizing associated data on phylogenetic tree using 'ggtree'. These associated data can be presented on the external panels to circular layout, fan layout, or other rectangular layout tree built by 'ggtree' with the grammar of 'ggplot2'.
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softwarevisualizationphylogeneticsannotation
10.60 score 98 stars 2 dependents 684 scripts 2.2k downloadsggstar - Multiple Geometric Shape Point Layer for 'ggplot2'
To create the multiple polygonal point layer for easily discernible shapes, we developed the package, it is like the 'geom_point' of 'ggplot2'. It can be used to draw the scatter plot.
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10.27 score 105 stars 6 dependents 514 scripts 2.1k downloadsMicrobiotaProcess - A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It introduces MPSE class, this make it more interoperable with the existing computing ecosystem. Moreover, it introduces a tidy microbiome data structure paradigm and analysis grammar. It provides a wide variety of microbiome data analysis procedures under the unified and common framework (tidy-like framework).
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visualizationmicrobiomesoftwaremultiplecomparisonfeatureextractionmicrobiome-analysismicrobiome-data
9.56 score 196 stars 223 scripts 812 downloadsSVP - Predicting cell states and their variability in single-cell or spatial omics data
SVP uses the distance between cells and cells, features and features, cells and features in the space of MCA to build nearest neighbor graph, then uses random walk with restart algorithm to calculate the activity score of gene sets (such as cell marker genes, kegg pathway, go ontology, gene modules, transcription factor or miRNA target sets, reactome pathway, ...), which is then further weighted using the hypergeometric test results from the original expression matrix. To detect the spatially or single cell variable gene sets or (other features) and the spatial colocalization between the features accurately, SVP provides some global and local spatial autocorrelation method to identify the spatial variable features. SVP is developed based on SingleCellExperiment class, which can be interoperable with the existing computing ecosystem.
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singlecellsoftwarespatialtranscriptomicsgenetargetgeneexpressiongenesetenrichmenttranscriptiongokeggopenblascppopenmp
5.56 score 12 stars 6 scripts 331 downloads