Contents

1 Summary of the output objects of scTensor

Here, we introduced the objects saved in reanalysis.RData.

suppressPackageStartupMessages(library("scTensor"))
load("reanalysis.RData")

After performing cellCellReport, some R objects are saved in the reanalysis.RData as follows;

2 Execution of scTensor with the different options

Using the reanalysis.RData, some user may want to perform scTensor with different parameters.

For example, the user can perform cellCellDecomp with different ranks, and also can peform cellCellReport with omiting some enrichment analysis step as follows.

suppressPackageStartupMessages(library("LRBase.Hsa.eg.db"))
# Register the file pass of user's LRBase
metadata(sce)$lrbase <- dbfile(LRBase.Hsa.eg.db)
# CCI Tensor Decomposition
cellCellDecomp(sce, ranks=c(6,5), assayNames="normcounts")
# HTML Report
cellCellReport(sce, reducedDimNames="TSNE", assayNames="normcounts",
    title="Cell-cell interaction within Germline_Male, GSE86146",
    author="Koki Tsuyuzaki", html.open=TRUE,
    goenrich=TRUE, meshenrich=FALSE, reactomeenrich=FALSE,
    doenrich=FALSE, ncgenrich=FALSE, dgnenrich=FALSE)

Session information

## R version 3.6.1 (2019-07-05)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows Server 2012 R2 x64 (build 9600)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=C                          
## [2] LC_CTYPE=English_United States.1252   
## [3] LC_MONETARY=English_United States.1252
## [4] LC_NUMERIC=C                          
## [5] LC_TIME=English_United States.1252    
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] AnnotationHub_2.18.0                   
##  [2] BiocFileCache_1.10.2                   
##  [3] dbplyr_1.4.2                           
##  [4] Homo.sapiens_1.3.1                     
##  [5] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
##  [6] org.Hs.eg.db_3.10.0                    
##  [7] GO.db_3.10.0                           
##  [8] OrganismDbi_1.28.0                     
##  [9] GenomicFeatures_1.38.0                 
## [10] AnnotationDbi_1.48.0                   
## [11] MeSH.Mmu.eg.db_1.13.0                  
## [12] LRBase.Mmu.eg.db_1.2.0                 
## [13] MeSH.Hsa.eg.db_1.13.0                  
## [14] MeSHDbi_1.22.0                         
## [15] SingleCellExperiment_1.8.0             
## [16] SummarizedExperiment_1.16.0            
## [17] DelayedArray_0.12.0                    
## [18] BiocParallel_1.20.0                    
## [19] matrixStats_0.55.0                     
## [20] Biobase_2.46.0                         
## [21] GenomicRanges_1.38.0                   
## [22] GenomeInfoDb_1.22.0                    
## [23] IRanges_2.20.0                         
## [24] S4Vectors_0.24.0                       
## [25] BiocGenerics_0.32.0                    
## [26] scTensor_1.2.1                         
## [27] RSQLite_2.1.2                          
## [28] LRBase.Hsa.eg.db_1.2.0                 
## [29] LRBaseDbi_1.4.0                        
## [30] BiocStyle_2.14.0                       
## 
## loaded via a namespace (and not attached):
##   [1] rappdirs_0.3.1                rtracklayer_1.46.0           
##   [3] AnnotationForge_1.28.0        tidyr_1.0.0                  
##   [5] ggplot2_3.2.1                 acepack_1.4.1                
##   [7] bit64_0.9-7                   knitr_1.25                   
##   [9] data.table_1.12.6             rpart_4.1-15                 
##  [11] RCurl_1.95-4.12               AnnotationFilter_1.10.0      
##  [13] cowplot_1.0.0                 europepmc_0.3                
##  [15] bit_1.1-14                    enrichplot_1.6.0             
##  [17] webshot_0.5.1                 xml2_1.2.2                   
##  [19] httpuv_1.5.2                  assertthat_0.2.1             
##  [21] viridis_0.5.1                 xfun_0.10                    
##  [23] hms_0.5.2                     evaluate_0.14                
##  [25] promises_1.1.0                TSP_1.1-7                    
##  [27] progress_1.2.2                caTools_1.17.1.2             
##  [29] dendextend_1.12.0             Rgraphviz_2.30.0             
##  [31] igraph_1.2.4.1                DBI_1.0.0                    
##  [33] htmlwidgets_1.5.1             MeSH.db_1.13.0               
##  [35] purrr_0.3.3                   dplyr_0.8.3                  
##  [37] backports_1.1.5               bookdown_0.14                
##  [39] annotate_1.64.0               biomaRt_2.42.0               
##  [41] vctrs_0.2.0                   ensembldb_2.10.0             
##  [43] abind_1.4-5                   ggforce_0.3.1                
##  [45] Gviz_1.30.0                   triebeard_0.3.0              
##  [47] BSgenome_1.54.0               checkmate_1.9.4              
##  [49] GenomicAlignments_1.22.0      gclus_1.3.2                  
##  [51] fdrtool_1.2.15                prettyunits_1.0.2            
##  [53] cluster_2.1.0                 DOSE_3.12.0                  
##  [55] dotCall64_1.0-0               lazyeval_0.2.2               
##  [57] crayon_1.3.4                  genefilter_1.68.0            
##  [59] pkgconfig_2.0.3               tweenr_1.0.1                 
##  [61] ProtGenerics_1.18.0           seriation_1.2-8              
##  [63] nnet_7.3-12                   rlang_0.4.1                  
##  [65] lifecycle_0.1.0               meshr_1.22.0                 
##  [67] registry_0.5-1                MeSH.PCR.db_1.13.0           
##  [69] rTensor_1.4                   GOstats_2.52.0               
##  [71] dichromat_2.0-0               polyclip_1.10-0              
##  [73] graph_1.64.0                  Matrix_1.2-17                
##  [75] urltools_1.7.3                base64enc_0.1-3              
##  [77] ggridges_0.5.1                viridisLite_0.3.0            
##  [79] MeSH.AOR.db_1.13.0            bitops_1.0-6                 
##  [81] visNetwork_2.0.8              KernSmooth_2.23-16           
##  [83] spam_2.4-0                    MeSH.Bsu.168.eg.db_1.13.0    
##  [85] Biostrings_2.54.0             blob_1.2.0                   
##  [87] stringr_1.4.0                 qvalue_2.18.0                
##  [89] nnTensor_1.0.2                gridGraphics_0.4-1           
##  [91] reactome.db_1.70.0            scales_1.0.0                 
##  [93] graphite_1.32.0               memoise_1.1.0                
##  [95] GSEABase_1.48.0               magrittr_1.5                 
##  [97] plyr_1.8.4                    gplots_3.0.1.1               
##  [99] gdata_2.18.0                  zlibbioc_1.32.0              
## [101] compiler_3.6.1                RColorBrewer_1.1-2           
## [103] plotrix_3.7-6                 Rsamtools_2.2.1              
## [105] XVector_0.26.0                Category_2.52.1              
## [107] MeSH.Aca.eg.db_1.13.0         htmlTable_1.13.2             
## [109] Formula_1.2-3                 MASS_7.3-51.4                
## [111] tidyselect_0.2.5              stringi_1.4.3                
## [113] highr_0.8                     MeSH.Syn.eg.db_1.13.0        
## [115] yaml_2.2.0                    GOSemSim_2.12.0              
## [117] askpass_1.1                   latticeExtra_0.6-28          
## [119] ggrepel_0.8.1                 grid_3.6.1                   
## [121] VariantAnnotation_1.32.0      fastmatch_1.1-0              
## [123] tools_3.6.1                   rstudioapi_0.10              
## [125] foreach_1.4.7                 foreign_0.8-72               
## [127] tagcloud_0.6                  outliers_0.14                
## [129] gridExtra_2.3                 farver_1.1.0                 
## [131] ggraph_2.0.0                  rvcheck_0.1.6                
## [133] digest_0.6.22                 BiocManager_1.30.9           
## [135] shiny_1.4.0                   Rcpp_1.0.3                   
## [137] BiocVersion_3.10.1            later_1.0.0                  
## [139] httr_1.4.1                    cummeRbund_2.28.0            
## [141] biovizBase_1.34.0             colorspace_1.4-1             
## [143] XML_3.98-1.20                 splines_3.6.1                
## [145] fields_9.9                    RBGL_1.62.1                  
## [147] graphlayouts_0.5.0            ggplotify_0.0.4              
## [149] plotly_4.9.1                  xtable_1.8-4                 
## [151] jsonlite_1.6                  heatmaply_0.16.0             
## [153] tidygraph_1.1.2               zeallot_0.1.0                
## [155] R6_2.4.0                      Hmisc_4.3-0                  
## [157] pillar_1.4.2                  htmltools_0.4.0              
## [159] mime_0.7                      glue_1.3.1                   
## [161] fastmap_1.0.1                 interactiveDisplayBase_1.24.0
## [163] codetools_0.2-16              maps_3.3.0                   
## [165] fgsea_1.12.0                  lattice_0.20-38              
## [167] tibble_2.1.3                  curl_4.2                     
## [169] gtools_3.8.1                  ReactomePA_1.30.0            
## [171] misc3d_0.8-4                  openssl_1.4.1                
## [173] survival_3.1-7                rmarkdown_1.16               
## [175] munsell_0.5.0                 DO.db_2.9                    
## [177] GenomeInfoDbData_1.2.2        plot3D_1.1.1                 
## [179] iterators_1.0.12              reshape2_1.4.3               
## [181] gtable_0.3.0