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 4.0.0 (2020-04-24)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.11-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.11-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] AnnotationHub_2.20.0                   
##  [2] BiocFileCache_1.12.0                   
##  [3] dbplyr_1.4.4                           
##  [4] Homo.sapiens_1.3.1                     
##  [5] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
##  [6] org.Hs.eg.db_3.11.4                    
##  [7] GO.db_3.11.4                           
##  [8] OrganismDbi_1.30.0                     
##  [9] GenomicFeatures_1.40.0                 
## [10] AnnotationDbi_1.50.0                   
## [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_1.24.0                         
## [15] SingleCellExperiment_1.10.1            
## [16] SummarizedExperiment_1.18.1            
## [17] DelayedArray_0.14.0                    
## [18] matrixStats_0.56.0                     
## [19] Biobase_2.48.0                         
## [20] GenomicRanges_1.40.0                   
## [21] GenomeInfoDb_1.24.2                    
## [22] IRanges_2.22.2                         
## [23] S4Vectors_0.26.1                       
## [24] BiocGenerics_0.34.0                    
## [25] scTensor_1.4.3                         
## [26] RSQLite_2.2.0                          
## [27] LRBase.Hsa.eg.db_1.2.0                 
## [28] LRBaseDbi_1.6.0                        
## [29] BiocStyle_2.16.0                       
## 
## loaded via a namespace (and not attached):
##   [1] rsvd_1.0.3                    Hmisc_4.4-0                  
##   [3] ica_1.0-2                     Rsamtools_2.4.0              
##   [5] foreach_1.5.0                 lmtest_0.9-37                
##   [7] crayon_1.3.4                  MASS_7.3-51.6                
##   [9] nlme_3.1-148                  backports_1.1.8              
##  [11] GOSemSim_2.14.0               rlang_0.4.6                  
##  [13] XVector_0.28.0                ROCR_1.0-11                  
##  [15] irlba_2.3.3                   nnTensor_1.0.5               
##  [17] GOstats_2.54.0                BiocParallel_1.22.0          
##  [19] tagcloud_0.6                  bit64_0.9-7                  
##  [21] glue_1.4.1                    sctransform_0.2.1            
##  [23] dotCall64_1.0-0               DOSE_3.14.0                  
##  [25] tidyselect_1.1.0              fitdistrplus_1.1-1           
##  [27] XML_3.99-0.3                  tidyr_1.1.0                  
##  [29] zoo_1.8-8                     GenomicAlignments_1.24.0     
##  [31] xtable_1.8-4                  magrittr_1.5                 
##  [33] evaluate_0.14                 ggplot2_3.3.2                
##  [35] zlibbioc_1.34.0               rstudioapi_0.11              
##  [37] rpart_4.1-15                  fastmatch_1.1-0              
##  [39] ensembldb_2.12.1              maps_3.3.0                   
##  [41] fields_10.3                   shiny_1.5.0                  
##  [43] xfun_0.15                     askpass_1.1                  
##  [45] cluster_2.1.0                 caTools_1.18.0               
##  [47] tidygraph_1.2.0               TSP_1.1-10                   
##  [49] tibble_3.0.1                  interactiveDisplayBase_1.26.3
##  [51] ggrepel_0.8.2                 biovizBase_1.36.0            
##  [53] ape_5.4                       listenv_0.8.0                
##  [55] dendextend_1.13.4             Biostrings_2.56.0            
##  [57] png_0.1-7                     future_1.17.0                
##  [59] bitops_1.0-6                  ggforce_0.3.2                
##  [61] RBGL_1.64.0                   plyr_1.8.6                   
##  [63] GSEABase_1.50.1               AnnotationFilter_1.12.0      
##  [65] pillar_1.4.4                  gplots_3.0.3                 
##  [67] graphite_1.34.0               europepmc_0.4                
##  [69] vctrs_0.3.1                   ellipsis_0.3.1               
##  [71] generics_0.0.2                plot3D_1.3                   
##  [73] urltools_1.7.3                MeSH.Aca.eg.db_1.13.0        
##  [75] outliers_0.14                 tools_4.0.0                  
##  [77] foreign_0.8-80                entropy_1.2.1                
##  [79] munsell_0.5.0                 tweenr_1.0.1                 
##  [81] fgsea_1.14.0                  fastmap_1.0.1                
##  [83] compiler_4.0.0                abind_1.4-5                  
##  [85] httpuv_1.5.4                  rtracklayer_1.48.0           
##  [87] Gviz_1.32.0                   plotly_4.9.2.1               
##  [89] GenomeInfoDbData_1.2.3        gridExtra_2.3                
##  [91] lattice_0.20-41               visNetwork_2.0.9             
##  [93] AnnotationForge_1.30.1        later_1.1.0.1                
##  [95] dplyr_1.0.0                   jsonlite_1.7.0               
##  [97] concaveman_1.1.0              scales_1.1.1                 
##  [99] graph_1.66.0                  pbapply_1.4-2                
## [101] genefilter_1.70.0             lazyeval_0.2.2               
## [103] promises_1.1.1                MeSH.db_1.13.0               
## [105] latticeExtra_0.6-29           reticulate_1.16              
## [107] checkmate_2.0.0               rmarkdown_2.3                
## [109] cowplot_1.0.0                 schex_1.2.0                  
## [111] MeSH.Syn.eg.db_1.13.0         webshot_0.5.2                
## [113] Rtsne_0.15                    dichromat_2.0-0              
## [115] BSgenome_1.56.0               uwot_0.1.8                   
## [117] igraph_1.2.5                  gclus_1.3.2                  
## [119] survival_3.2-3                yaml_2.2.1                   
## [121] plotrix_3.7-8                 htmltools_0.5.0              
## [123] memoise_1.1.0                 VariantAnnotation_1.34.0     
## [125] rTensor_1.4.1                 Seurat_3.1.5                 
## [127] seriation_1.2-8               graphlayouts_0.7.0           
## [129] viridisLite_0.3.0             digest_0.6.25                
## [131] assertthat_0.2.1              ReactomePA_1.32.0            
## [133] mime_0.9                      rappdirs_0.3.1               
## [135] registry_0.5-1                spam_2.5-1                   
## [137] future.apply_1.5.0            misc3d_0.8-4                 
## [139] data.table_1.12.8             blob_1.2.1                   
## [141] cummeRbund_2.30.0             splines_4.0.0                
## [143] Formula_1.2-3                 ProtGenerics_1.20.0          
## [145] RCurl_1.98-1.2                hms_0.5.3                    
## [147] colorspace_1.4-1              base64enc_0.1-3              
## [149] BiocManager_1.30.10           nnet_7.3-14                  
## [151] Rcpp_1.0.4.6                  bookdown_0.20                
## [153] RANN_2.6.1                    MeSH.PCR.db_1.13.0           
## [155] enrichplot_1.8.1              R6_2.4.1                     
## [157] grid_4.0.0                    ggridges_0.5.2               
## [159] lifecycle_0.2.0               acepack_1.4.1                
## [161] curl_4.3                      MeSH.Bsu.168.eg.db_1.13.0    
## [163] gdata_2.18.0                  leiden_0.3.3                 
## [165] MeSH.AOR.db_1.13.0            meshr_1.24.1                 
## [167] DO.db_2.9                     Matrix_1.2-18                
## [169] qvalue_2.20.0                 RcppAnnoy_0.0.16             
## [171] RColorBrewer_1.1-2            iterators_1.0.12             
## [173] stringr_1.4.0                 htmlwidgets_1.5.1            
## [175] polyclip_1.10-0               triebeard_0.3.0              
## [177] biomaRt_2.44.1                purrr_0.3.4                  
## [179] gridGraphics_0.5-0            reactome.db_1.70.0           
## [181] globals_0.12.5                openssl_1.4.2                
## [183] htmlTable_2.0.0               patchwork_1.0.1              
## [185] codetools_0.2-16              gtools_3.8.2                 
## [187] prettyunits_1.1.1             gtable_0.3.0                 
## [189] tsne_0.1-3                    DBI_1.1.0                    
## [191] highr_0.8                     httr_1.4.1                   
## [193] KernSmooth_2.23-17            stringi_1.4.6                
## [195] progress_1.2.2                reshape2_1.4.4               
## [197] farver_2.0.3                  heatmaply_1.1.0              
## [199] annotate_1.66.0               viridis_0.5.1                
## [201] hexbin_1.28.1                 fdrtool_1.2.15               
## [203] Rgraphviz_2.32.0              magick_2.4.0                 
## [205] xml2_1.3.2                    rvcheck_0.1.8                
## [207] ggplotify_0.0.5               Category_2.54.0              
## [209] BiocVersion_3.11.1            bit_1.1-15.2                 
## [211] scatterpie_0.1.4              jpeg_0.1-8.1                 
## [213] ggraph_2.0.3                  pkgconfig_2.0.3              
## [215] knitr_1.29