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 users may want to perform scTensor with different parameters.

For example, some users want to perform cellCellDecomp with different ranks, perform cellCellReport with omitting some enrichment analysis, provide the results to their collaborators.

To do such tasks, just type like belows.

if(!require(LRBase.Hsa.eg.db)){
    BiocManager::install("LRBase.Hsa.eg.db")
    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 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.5 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.12-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.12-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_2.22.0                   
##  [2] BiocFileCache_1.14.0                   
##  [3] dbplyr_1.4.4                           
##  [4] scTGIF_1.4.0                           
##  [5] Homo.sapiens_1.3.1                     
##  [6] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
##  [7] org.Hs.eg.db_3.12.0                    
##  [8] GO.db_3.12.0                           
##  [9] OrganismDbi_1.32.0                     
## [10] GenomicFeatures_1.42.0                 
## [11] AnnotationDbi_1.52.0                   
## [12] LRBase.Mmu.eg.db_1.2.0                 
## [13] SingleCellExperiment_1.12.0            
## [14] SummarizedExperiment_1.20.0            
## [15] Biobase_2.50.0                         
## [16] GenomicRanges_1.42.0                   
## [17] GenomeInfoDb_1.26.0                    
## [18] IRanges_2.24.0                         
## [19] S4Vectors_0.28.0                       
## [20] BiocGenerics_0.36.0                    
## [21] MatrixGenerics_1.2.0                   
## [22] matrixStats_0.57.0                     
## [23] scTensor_2.0.0                         
## [24] RSQLite_2.2.1                          
## [25] LRBase.Hsa.eg.db_1.2.0                 
## [26] LRBaseDbi_2.0.0                        
## [27] BiocStyle_2.18.0                       
## 
## loaded via a namespace (and not attached):
##   [1] rsvd_1.0.3                    Hmisc_4.4-1                  
##   [3] ica_1.0-2                     Rsamtools_2.6.0              
##   [5] foreach_1.5.1                 lmtest_0.9-38                
##   [7] crayon_1.3.4                  MASS_7.3-53                  
##   [9] nlme_3.1-150                  backports_1.1.10             
##  [11] GOSemSim_2.16.0               MeSHDbi_1.26.0               
##  [13] rlang_0.4.8                   XVector_0.30.0               
##  [15] ROCR_1.0-11                   irlba_2.3.3                  
##  [17] nnTensor_1.0.5                GOstats_2.56.0               
##  [19] BiocParallel_1.24.0           tagcloud_0.6                 
##  [21] bit64_4.0.5                   glue_1.4.2                   
##  [23] sctransform_0.3.1             dotCall64_1.0-0              
##  [25] tcltk_4.0.3                   DOSE_3.16.0                  
##  [27] tidyselect_1.1.0              fitdistrplus_1.1-1           
##  [29] XML_3.99-0.5                  tidyr_1.1.2                  
##  [31] zoo_1.8-8                     GenomicAlignments_1.26.0     
##  [33] xtable_1.8-4                  magrittr_1.5                 
##  [35] evaluate_0.14                 ggplot2_3.3.2                
##  [37] zlibbioc_1.36.0               rstudioapi_0.11              
##  [39] miniUI_0.1.1.1                rpart_4.1-15                 
##  [41] fastmatch_1.1-0               ensembldb_2.14.0             
##  [43] maps_3.3.0                    fields_11.6                  
##  [45] shiny_1.5.0                   xfun_0.18                    
##  [47] askpass_1.1                   cluster_2.1.0                
##  [49] tidygraph_1.2.0               TSP_1.1-10                   
##  [51] tibble_3.0.4                  interactiveDisplayBase_1.28.0
##  [53] ggrepel_0.8.2                 biovizBase_1.38.0            
##  [55] listenv_0.8.0                 dendextend_1.14.0            
##  [57] Biostrings_2.58.0             png_0.1-7                    
##  [59] future_1.19.1                 bitops_1.0-6                 
##  [61] ggforce_0.3.2                 RBGL_1.66.0                  
##  [63] plyr_1.8.6                    GSEABase_1.52.0              
##  [65] AnnotationFilter_1.14.0       pillar_1.4.6                 
##  [67] graphite_1.36.0               vctrs_0.3.4                  
##  [69] ellipsis_0.3.1                generics_0.0.2               
##  [71] plot3D_1.3                    MeSH.Aca.eg.db_1.13.0        
##  [73] outliers_0.14                 tools_4.0.3                  
##  [75] foreign_0.8-80                entropy_1.2.1                
##  [77] munsell_0.5.0                 tweenr_1.0.1                 
##  [79] fgsea_1.16.0                  DelayedArray_0.16.0          
##  [81] fastmap_1.0.1                 compiler_4.0.3               
##  [83] abind_1.4-5                   httpuv_1.5.4                 
##  [85] rtracklayer_1.50.0            Gviz_1.34.0                  
##  [87] plotly_4.9.2.1                GenomeInfoDbData_1.2.4       
##  [89] gridExtra_2.3                 lattice_0.20-41              
##  [91] deldir_0.1-29                 visNetwork_2.0.9             
##  [93] AnnotationForge_1.32.0        later_1.1.0.1                
##  [95] dplyr_1.0.2                   jsonlite_1.7.1               
##  [97] concaveman_1.1.0              scales_1.1.1                 
##  [99] graph_1.68.0                  pbapply_1.4-3                
## [101] genefilter_1.72.0             lazyeval_0.2.2               
## [103] promises_1.1.1                spatstat_1.64-1              
## [105] MeSH.db_1.13.0                latticeExtra_0.6-29          
## [107] goftest_1.2-2                 spatstat.utils_1.17-0        
## [109] reticulate_1.18               checkmate_2.0.0              
## [111] rmarkdown_2.5                 cowplot_1.1.0                
## [113] schex_1.4.0                   MeSH.Syn.eg.db_1.13.0        
## [115] webshot_0.5.2                 Rtsne_0.15                   
## [117] dichromat_2.0-0               BSgenome_1.58.0              
## [119] uwot_0.1.8                    igraph_1.2.6                 
## [121] survival_3.2-7                yaml_2.2.1                   
## [123] plotrix_3.7-8                 htmltools_0.5.0              
## [125] memoise_1.1.0                 VariantAnnotation_1.36.0     
## [127] rTensor_1.4.1                 Seurat_3.2.2                 
## [129] seriation_1.2-9               graphlayouts_0.7.1           
## [131] viridisLite_0.3.0             digest_0.6.27                
## [133] assertthat_0.2.1              ReactomePA_1.34.0            
## [135] mime_0.9                      rappdirs_0.3.1               
## [137] registry_0.5-1                spam_2.5-1                   
## [139] future.apply_1.6.0            misc3d_0.9-0                 
## [141] data.table_1.13.2             blob_1.2.1                   
## [143] cummeRbund_2.32.0             splines_4.0.3                
## [145] Formula_1.2-4                 ProtGenerics_1.22.0          
## [147] RCurl_1.98-1.2                hms_0.5.3                    
## [149] colorspace_1.4-1              base64enc_0.1-3              
## [151] BiocManager_1.30.10           nnet_7.3-14                  
## [153] Rcpp_1.0.5                    bookdown_0.21                
## [155] RANN_2.6.1                    MeSH.PCR.db_1.13.0           
## [157] enrichplot_1.10.0             R6_2.4.1                     
## [159] grid_4.0.3                    ggridges_0.5.2               
## [161] lifecycle_0.2.0               curl_4.3                     
## [163] MeSH.Bsu.168.eg.db_1.13.0     leiden_0.3.3                 
## [165] MeSH.AOR.db_1.13.0            meshr_1.26.0                 
## [167] DO.db_2.9                     Matrix_1.2-18                
## [169] qvalue_2.22.0                 RcppAnnoy_0.0.16             
## [171] RColorBrewer_1.1-2            iterators_1.0.13             
## [173] stringr_1.4.0                 htmlwidgets_1.5.2            
## [175] polyclip_1.10-0               biomaRt_2.46.0               
## [177] purrr_0.3.4                   shadowtext_0.0.7             
## [179] reactome.db_1.74.0            mgcv_1.8-33                  
## [181] globals_0.13.1                openssl_1.4.3                
## [183] htmlTable_2.1.0               patchwork_1.0.1              
## [185] codetools_0.2-16              prettyunits_1.1.1            
## [187] gtable_0.3.0                  DBI_1.1.0                    
## [189] tensor_1.5                    httr_1.4.2                   
## [191] highr_0.8                     KernSmooth_2.23-17           
## [193] stringi_1.5.3                 progress_1.2.2               
## [195] msigdbr_7.2.1                 reshape2_1.4.4               
## [197] farver_2.0.3                  heatmaply_1.1.1              
## [199] annotate_1.68.0               viridis_0.5.1                
## [201] hexbin_1.28.1                 fdrtool_1.2.15               
## [203] Rgraphviz_2.34.0              magick_2.5.0                 
## [205] xml2_1.3.2                    rvcheck_0.1.8                
## [207] Category_2.56.0               BiocVersion_3.12.0           
## [209] bit_4.0.4                     scatterpie_0.1.5             
## [211] jpeg_0.1-8.1                  spatstat.data_1.4-3          
## [213] ggraph_2.0.3                  pkgconfig_2.0.3              
## [215] MeSH.Hsa.eg.db_1.13.0         knitr_1.30