scTensor 2.0.0
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;
cellCellSettingcellCellSettingUsing 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)## 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