Package: AnanseSeurat 1.2.0

Jos Smits

AnanseSeurat: Construct ANANSE GRN-Analysis Seurat

Enables gene regulatory network (GRN) analysis on single cell clusters, using the GRN analysis software 'ANANSE', Xu et al.(2021) <doi:10.1093/nar/gkab598>. Export data from 'Seurat' objects, for GRN analysis by 'ANANSE' implemented in 'snakemake'. Finally, incorporate results for visualization and interpretation.

Authors:Jos Smits [aut, cre, cph], Huiqing Jo Zhou [aut, fnd, cph]

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Peer review:

Bug tracker:https://github.com/jgasmits/ananseseurat/issues

On CRAN:

grn-analysisseurat-objectssingle-cellsingle-cell-atac-seqsingle-cell-rna-seq

11 exports 8 stars 1.59 score 170 dependencies 4 scripts 1.2k downloads

Last updated 10 months agofrom:3e46630a24. Checks:OK: 7. Indexed: yes.

Exports:%>%config_scANANSEDEGS_scANANSEexport_ATAC_maelstromexport_ATAC_scANANSEexport_CPM_scANANSEFactor_Motif_Plotimport_seurat_maelstromimport_seurat_scANANSEMaelstrom_Motif2TFper_cluster_df

Dependencies:abindaskpassbackportsbase64encBHbitopsbootbroombslibcachemcarcarDatacaToolscliclustercodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncrosstalkcurldata.tabledeldirDerivdigestdoBydotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggpubrggrepelggridgesggsciggsignifglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlme4lmtestmagrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminiUIminqamodelrmunsellnlmenloptrnnetnumDerivopensslparallellypatchworkpbapplypbkrtestpillarpkgconfigplotlyplyrpngpolyclippolynomprogressrpromisespurrrquantregR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectrarstatixRtsnesassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamSparseMspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo