Package: MetaNeighbor 1.27.0

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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MetaNeighbor.pdf |MetaNeighbor.html✨
MetaNeighbor/json (API)
NEWS

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

Peer review:

Datasets:

On BioConductor:MetaNeighbor-1.27.0(bioc 3.21)MetaNeighbor-1.26.0(bioc 3.20)

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

immunooncologygeneexpressiongomultiplecomparisonsinglecelltranscriptomics

5.89 score 77 scripts 322 downloads 11 mentions 29 exports 69 dependencies

Last updated 23 days agofrom:7dda94c8b7. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 02 2024
R-4.5-winWARNINGNov 02 2024
R-4.5-linuxWARNINGNov 02 2024
R-4.4-winWARNINGNov 02 2024
R-4.4-macWARNINGNov 02 2024
R-4.3-winWARNINGNov 02 2024
R-4.3-macWARNINGNov 02 2024

Exports:extendClusterSetextractMetaClustersgetCellTypegetStudyIdggPlotHeatmapmakeClusterGraphmakeClusterNamemergeSCEMetaNeighborMetaNeighborUSneighborVotingorderCellTypesplotBPlotplotClusterGraphplotDotPlotplotHeatmapplotHeatmapPretrainedplotMetaClustersplotUpsetscoreMetaClusterssplitClusterssplitTestClusterssplitTrainClustersstandardizeLabelsubsetClusterGraphtopHitstopHitsByStudytrainModelvariableGenes

Dependencies:abindaskpassbeanplotBiobaseBiocGenericsbitopscaToolsclicolorspacecpp11crayoncurlDelayedArraydplyrfansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegplotsgtablegtoolshttrigraphIRangesisobandjsonliteKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigpurrrR6RColorBrewerrlangS4ArraysS4VectorsscalesSingleCellExperimentSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

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 Nov 02 2024.

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

Readme and manuals

Help Manual

Help pageTopics
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
GOhumanGOhuman
GOmouseGOmouse
Convert AUROC matrix into a graph.makeClusterGraph
Make cluster names in format 'study_id|cell_type'makeClusterName
Merge multiple SingleCellExperiment objects.mergeSCE
Runs MetaNeighborMetaNeighbor
Runs unsupervised version of MetaNeighborMetaNeighborUS
mn_datamn_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 conflictsstandardizeLabel
Subset cluster graph to clusters of interest.subsetClusterGraph
Find reciprocal top hitstopHits
Find reciprocal top hits, stratifying results by study.topHitsByStudy
Pretrains model for the unsupervised version of MetaNeighbortrainModel
Identify a highly variable gene setvariableGenes