Package: MetaNeighbor 1.25.0

Stephan Fischer

MetaNeighbor: Single cell replicability analysis

MetaNeighbor allows users to quantify cell type replicability across datasets using neighbor voting.

Authors:Megan Crow [aut, cre], Sara Ballouz [ctb], Manthan Shah [ctb], Stephan Fischer [ctb], Jesse Gillis [aut]

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NEWS

# Install 'MetaNeighbor' in R:

install.packages('MetaNeighbor', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

GOhuman - GOhuman
GOmouse - GOmouse
mn_data - Mn_data

On BioConductor:MetaNeighbor-1.25.0(bioc 3.20)MetaNeighbor-1.24.0(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

29 exports 1.08 score 69 dependencies 11 mentions

Last updated 2 months agofrom:f7aeeffe7a

Exports:extendClusterSet extractMetaClusters getCellType getStudyId ggPlotHeatmap makeClusterGraph makeClusterName mergeSCE MetaNeighbor MetaNeighborUS neighborVoting orderCellTypes plotBPlot plotClusterGraph plotDotPlot plotHeatmap plotHeatmapPretrained plotMetaClusters plotUpset scoreMetaClusters splitClusters splitTestClusters splitTrainClusters standardizeLabel subsetClusterGraph topHits topHitsByStudy trainModel variableGenes

Dependencies:abind askpass beanplot Biobase BiocGenerics bitops caTools cli colorspace cpp11 crayon curl DelayedArray dplyr fansi farver generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gplots gtable gtools httr igraph IRanges isoband jsonlite KernSmooth labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig purrr R6 RColorBrewer rlang S4Arrays S4Vectors scales SingleCellExperiment SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

MetaNeighbor : a method to rapidly assess cell type identity using both functional and random gene sets

Megan Crow, Stephan Fischer, Sara Ballouz, Manthan Shah, Jesse Gillis

Rendered fromMetaNeighbor.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2019-05-01
Started: 2017-10-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Extend cluster set to nearest neighbors on cluster graph.	extendClusterSet
Extracts groups of reciprocal top hits from a 1-vs-best AUROC matrix.	extractMetaClusters
Return cell type from a label in format 'study_id\|cell_type'	getCellType
Return study ID from a label in format 'study_id\|cell_type'	getStudyId
Plots symmetric AUROC heatmap, clustering cell types by similarity.	ggPlotHeatmap
GOhuman	GOhuman
GOmouse	GOmouse
Convert AUROC matrix into a graph.	makeClusterGraph
Make cluster names in format 'study_id\|cell_type'	makeClusterName
Merge multiple SingleCellExperiment objects.	mergeSCE
Runs MetaNeighbor	MetaNeighbor
Runs unsupervised version of MetaNeighbor	MetaNeighborUS
mn_data	mn_data
Runs the neighbor voting algorithm.	neighborVoting
Order cell types based on AUROC similarity matrix.	orderCellTypes
Plot Bean Plot, showing how replicability of cell types depends on gene sets.	plotBPlot
Plot cluster graph generated with makeClusterGraph.	plotClusterGraph
Plot dot plot showing expression of a gene set across cell types.	plotDotPlot
Plots symmetric AUROC heatmap, clustering cell types by similarity.	plotHeatmap
Plots rectangular AUROC heatmap, clustering train cell types (columns) by similarity, and ordering test cell types (rows) according to similarity to train cell types..	plotHeatmapPretrained
Plot meta-cluster badges, each badge is a small AUROC heatmap restricted to a specific meta-cluster.	plotMetaClusters
Plot Upset plot showing how replicability depends on input dataset.	plotUpset
Summarize meta-cluster information in a table.	scoreMetaClusters
Split clusters according to symmetric AUROC similarity.	splitClusters
Split test clusters according to AUROC similarity to train clusters.	splitTestClusters
Split train clusters according to AUROC similarity to test clusters.	splitTrainClusters
Remove special characters ("\|") from labels to avoid later conflicts	standardizeLabel
Subset cluster graph to clusters of interest.	subsetClusterGraph
Find reciprocal top hits	topHits
Find reciprocal top hits, stratifying results by study.	topHitsByStudy
Pretrains model for the unsupervised version of MetaNeighbor	trainModel
Identify a highly variable gene set	variableGenes