VERSION 2.4.1 ------------------------ o A vignette modified. VERSION 2.4.0 ------------------------ o Regularizer parameter (L2_A/L1_A) was added in cellCellDecomp() ("ntd", "ntd2"). o Multilinear CX Decompotision was added in cellCellDecomp() ("cx"). o convertNCBIGeneID is removed. o The vignettes were modified. o Support of LRBase.XXX.eg.db-type packages is completely deprecated VERSION 2.0.0 ------------------------ o Extended to use the version 2.0.0 of LRBase.XXX.eg.db-type packages o Omitted typing Enter-key many times to perform example('cellCellReport') o lr.evidence option was added in cellCellRanks() and cellCellDecomp() to select ligand-receptor databases to construct CCI-tensor (cf. Evidence code: https://github.com/rikenbit/lrbase-workflow) o The L-R evidence was embeded in the HTML report. o The bug related to the hyper-link was fixed in .hyperLinks. o Auto library installation/loading for MeSH.XXX.eg.db. Note that this function is based on the NCBI Taxonomy ID embedded in METATDATA table in the sqlite3 file of LRBase.XXX.eg.db. o The order of the parameters of cellCellSetting were changed as cellCellSetting(sce, lrbase, label, lr.evidence="all", color=NULL), and color parameter was changed as a optional parameter. If it is not specified, the color is automatically selected. o The way to specify the celltype label was changed in cellCellSetting. o The vignettes were modified. o The convertNCBIGeneID is deprecated. The same functionality can be available as scTGIF::convertRowID instead. VERSION 1.4.1-3 ------------------------ o A bug was fixed in .cellCellDecomp.Halpern() VERSION 1.4.0 (Bioconductor 3.11) ------------------------ o verbose parameter was added in cellCellRank() and cellCellDecomp() o set.seed(1234) was added in example and vignette o .cellCellDecomp.CabelloAguilar() and .cellCellDecomp.Halpern() were added o The num.iter 300 of NTD was changed to 30 o schex package was imported for visualing all the two dimensional gene plots o The rule of cellCellRanks() based on the singular value of SVD was changed to a reconstruction error based rule, using NMF with matricised tensor in each mode o The CCI-tensor is normalized in each frontral slice so that the total value is 1 (.frontal.normalization) VERSION 1.2.1 ------------------------ o Some bugs were fixed VERSION 1.2.0 (Bioconductor 3.10) ------------------------ o goenrich, meshenrich, reactomeenrich, doenrich, ncgenrich, and dgnenrich in cellCellReport() were added o A bug related in sparse matrix in cellCellSetting() was fixed o All the vignettes were updated o A vignette for reanalysis of the results of scTensor was added o Some bugs were fixed VERSION 1.0.13 ------------------------ o Gene-gene network based on visNetwork was introduced VERSION 1.0.11 - 1.0.12 ------------------------ o Some bugs were fixed VERSION 1.0.10 ------------------------ o The tensor decomposition model was changed from non-negative Tucker3 to non-negative Tucker2 o assayNames option was added to specify which normalized assay data user want to use o ftt option was removed (any normalization can be performed instead) VERSION 1.0.7 - 1.0.9 ------------------------ o Some bugs were fixed VERSION 1.0.6 ------------------------ o Replaced Dependency against biomaRt by AnnotationHub VERSION 1.0.3 - 1.0.5 ------------------------ o Some bugs were fixed VERSION 1.0.2 ------------------------ o Added upper in cellCellReport() o Table grid lines in {ligand,receptor}*.Rmd were added o Some bugs were fixed VERSION 1.0.1 ------------------------ o Some bugs were fixed o Three vignettes were added o convertToNCBIGeneID() to ID conversion of input matrix VERSION 1.0.0 (Bioconductor 3.9) ------------------------ o Package release VERSION 0.99.22 ------------------------ o newCCSParams(), getParam(), setParam(), and cellCellSimulate() were added o The hyperlinks to CMap (Connectivity Map) were embedded in the HTML report VERSION 0.99.21 ------------------------ o Some bugs were fixed VERSION 0.99.18 ------------------------ o Added Enrichment Analysis in cellCellReport() VERSION 0.99.15 ------------------------ o Accepted in BioC 3.9 VERSION 0.99.6 to 0.99.14 ------------------------ o Revised and modified some parts VERSION 0.99.0 ------------------------ o Package released