Package: conos 1.5.2

Evan Biederstedt

conos: Clustering on Network of Samples

Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.

Authors:Viktor Petukhov [aut], Nikolas Barkas [aut], Peter Kharchenko [aut], Weiliang Qiu [ctb], Evan Biederstedt [aut, cre]

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Peer review:

Bug tracker:https://github.com/kharchenkolab/conos/issues

On CRAN:

batch-correctionscrna-seqsingle-cell-rna-seq

40 exports 191 stars 5.40 score 81 dependencies 1 mentions 205 scripts 594 downloads

Last updated 7 months agofrom:91110bafc0. Checks:OK: 9. Indexed: yes.

Exports:basicSeuratProcbestClusterThresholdsbestClusterTreeThresholdsbuildWijMatrixConosconvertToPagoda2edgeMatedgeMat<-embeddingPlotestimateWeightEntropyPerCellfindSubcommunitiesgetBetweenCellTypeCorrectedDEgetBetweenCellTypeDEgetCellNamesgetClusteringgetCountMatrixgetEmbeddinggetGeneExpressiongetGenesgetOverdispersedGenesgetPcagetPerCellTypeDEgetRawCountMatrixgetSampleNamePerCellgreedyModularityCutleiden.communityp2app4conosplotClusterBarplotsplotClusterBoxPlotsByAppTypeplotComponentVarianceplotDEheatmapprojectKNNsrawMatricesWithCommonGenessaveConosForScanPysaveDEasCSVsaveDEasJSONscanKModularitysgdBatchesstableTreeClustersvelocityInfoConos

Dependencies:abindBHBiocGenericscirclizecliclueclustercodetoolscolorspaceComplexHeatmapcowplotcpp11crayondendextenddigestdoParalleldplyrdqrngfansifarverFNNforeachgenericsGetoptLongggplot2ggrepelGlobalOptionsgluegridExtragtableigraphIRangesirlbaisobanditeratorslabelinglatticeleidenAlglifecyclemagrittrMASSMatrixmatrixStatsmgcvmunsellN2RnlmepbmcapplypillarpkgconfigplyrpngpROCR6RColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressRcppSpdlogreshape2rjsonrlangRSpectraRtsneS4Vectorsscalessccoreshapesitmostringistringrtibbletidyselectutf8uwotvctrsviridisviridisLitewithr