VERSION 1.4.1-2 ------------------------ 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