CHANGES IN VERSION 1.17.6 ------------------------- o Add fragmentNameMap to createDataset. CHANGES IN VERSION 1.17.5 ------------------------- o Optimize read and save ATAC peak matrix. CHANGES IN VERSION 1.17.4 ------------------------- o Add module ExplorerAcc. CHANGES IN VERSION 1.17.3 ------------------------- o check parameters before creating dataset. CHANGES IN VERSION 1.17.2 ------------------------- o add binSize parameter for atac bigwig files. CHANGES IN VERSION 1.17.1 ------------------------- o fix the bug if no signals for atac coverage and invalid filenames. CHANGES IN VERSION 1.15.22 ------------------------- o add warning message to log file when the atac bigwig files are not available. CHANGES IN VERSION 1.15.21 ------------------------- o fix a bug that counter table is not available. CHANGES IN VERSION 1.15.20 ------------------------- o Add csv format for figure data download. CHANGES IN VERSION 1.15.19 ------------------------- o Try to handle the error `Timeout was reached: [www.ncbi.nlm.nih.gov] SSL/TLS connection timeout`. CHANGES IN VERSION 1.15.18 ------------------------- o add protection of column sampleID in cell info editor funcitons. CHANGES IN VERSION 1.15.17 ------------------------- o Error handle if metadata contains '|'. o add cell info editor funcitons. CHANGES IN VERSION 1.15.16 ------------------------- o add more download format. CHANGES IN VERSION 1.15.15 ------------------------- o fix the low resolution of the plot. CHANGES IN VERSION 1.15.14 ------------------------- o fix the dotplot download issue. CHANGES IN VERSION 1.15.13 ------------------------- o add detailed fontsize and font family control. o change the dotplot from ggplot2 to complexheatmap. CHANGES IN VERSION 1.15.12 ------------------------- o order the stacked violin plots by input order. CHANGES IN VERSION 1.15.11 ------------------------- o add reorder function for splitBy for violin plots. CHANGES IN VERSION 1.15.10 ------------------------- o add color picker. o add splitBy for violin plots. o fix the issue that refresh explorer will lost the subset info. CHANGES IN VERSION 1.15.9 ------------------------- o add help video playlist. CHANGES IN VERSION 1.15.8 ------------------------- o add functionality to allow different labels for cell info. o allow subset groups for explorer. CHANGES IN VERSION 1.15.7 ------------------------- o fix the issue of reload everything when edit the cell info. CHANGES IN VERSION 1.15.6 ------------------------- o Editable cell info during login mode. o Hiden the cells when check the hidden box. CHANGES IN VERSION 1.15.5 ------------------------- o Response to the download width and height. CHANGES IN VERSION 1.15.4 ------------------------- o Access tab via query string. CHANGES IN VERSION 1.15.3 ------------------------- o Access data via data title. CHANGES IN VERSION 1.15.2 ------------------------- o Add favicon. CHANGES IN VERSION 1.15.1 ------------------------- o Fix the unique vistor counter. CHANGES IN VERSION 1.3.25 ------------------------- o Fix the abstract issue for edit module. CHANGES IN VERSION 1.3.24 ------------------------- o Update the description. CHANGES IN VERSION 1.3.23 ------------------------- o Add a hyperlink to package URL at footer. CHANGES IN VERSION 1.3.22 ------------------------- o Fix the duplicated rownames. CHANGES IN VERSION 1.3.21 ------------------------- o Add search button in the home page. CHANGES IN VERSION 1.3.20 ------------------------- o Change the default waffle plot group to celltype. CHANGES IN VERSION 1.3.19 ------------------------- o Update abstract in the admin edit tab. CHANGES IN VERSION 1.3.18 ------------------------- o Add abstract parameter for createAppConfig CHANGES IN VERSION 1.3.17 ------------------------- o Fix the issue if no ip location information available when update from the older version. o add the possibility of the feature names to replace the rownames. CHANGES IN VERSION 1.3.16 ------------------------- o Fix the missmatch UI and ID. CHANGES IN VERSION 1.3.15 ------------------------- o Fix the no id column issue when update the database. CHANGES IN VERSION 1.3.14 ------------------------- o Update the maxOptions from 6 to 50. CHANGES IN VERSION 1.3.13 ------------------------- o Add groupby parameter for correlation for proportion plot. CHANGES IN VERSION 1.3.12 ------------------------- o Add correlation for proportion plot. CHANGES IN VERSION 1.3.11 ------------------------- o Add Wilcoxon test for violin plot. CHANGES IN VERSION 1.3.10 ------------------------- o Add Chisq test for proportion. CHANGES IN VERSION 1.3.9 ------------------------- o Fix some typos. CHANGES IN VERSION 1.3.8 ------------------------- o Change dependence from hdf5r to rhdf5. CHANGES IN VERSION 1.3.7 ------------------------- o Fix the wrong downloader handler in downloader module. CHANGES IN VERSION 1.3.6 ------------------------- o Add downloader module. CHANGES IN VERSION 1.3.5 ------------------------- o Add gene name map to sql database. CHANGES IN VERSION 1.3.4 ------------------------- o Fix the issue of missing stats for cell numbers. CHANGES IN VERSION 1.3.3 ------------------------- o Add user visit info and gene symbols into the sql database. CHANGES IN VERSION 1.3.2 ------------------------- o Add dataset configuration into the sql database. CHANGES IN VERSION 1.3.1 ------------------------- o Make it compatable with SeuratObject V5. CHANGES IN VERSION 1.1.10 ------------------------- o Fix the download button for the explorer module. CHANGES IN VERSION 1.1.9 ------------------------- o Fix the repeat retreive for reference by createAppConfig. CHANGES IN VERSION 1.1.8 ------------------------- o Change the filepath for credential file. CHANGES IN VERSION 1.1.7 ------------------------- o Fix the bug in scInit for datafolder. CHANGES IN VERSION 1.1.6 ------------------------- o Fix the download button which download the fixed values. o Add multiple subset buttons. CHANGES IN VERSION 1.1.5 ------------------------- o List the available datasets by users privilege. CHANGES IN VERSION 1.1.4 ------------------------- o Fix the bug if the data is removed where user is explorering. CHANGES IN VERSION 1.1.3 ------------------------- o Fix the bug introduced by changing actionBution to checkboxInput for modBubbleHeatmap. CHANGES IN VERSION 1.1.2 ------------------------- o Add multiple layer of violin plot o Add sample order controls for stats plot CHANGES IN VERSION 1.1.1 ------------------------- o Fix the bug that `coverage` function is not imported. CHANGES IN VERSION 0.99.27 ------------------------- o Fix the subtitles for scATACseq data. CHANGES IN VERSION 0.99.25 ------------------------- o Fix a typo when fixing the chromsome name style for scATACseq data. CHANGES IN VERSION 0.99.24 ------------------------- o Add tracks for scATACseq data. CHANGES IN VERSION 0.99.23 ------------------------- o Add title for ATAC plot buttons. CHANGES IN VERSION 0.99.22 ------------------------- o Fix the issue if there is no reference. CHANGES IN VERSION 0.99.21 ------------------------- o Fix the typo for `createDataset` function. CHANGES IN VERSION 0.99.20 ------------------------- o Add zoom in and out for atac track plots. CHANGES IN VERSION 0.99.19 ------------------------- o Update the atac track plots. CHANGES IN VERSION 0.99.18 ------------------------- o Simplify the about module. CHANGES IN VERSION 0.99.17 ------------------------- o Update documentation for cellgene VIP. CHANGES IN VERSION 0.99.16 ------------------------- o fix the bug for cell index for waffleplot. CHANGES IN VERSION 0.99.15 ------------------------- o fix the bug if no reference can be retrieved. CHANGES IN VERSION 0.99.14 ------------------------- o fix the bug if no markers can be detected. CHANGES IN VERSION 0.99.13 ------------------------- o remove aes_string. CHANGES IN VERSION 0.99.12 ------------------------- o fix the dropdown names issue. CHANGES IN VERSION 0.99.11 ------------------------- o add check/uncheck all to subset cells. CHANGES IN VERSION 0.99.10 ------------------------- o fix the multiple loading. CHANGES IN VERSION 0.99.9 ------------------------- o fix the long table in vignette. CHANGES IN VERSION 0.99.8 ------------------------- o add app_path to app to fix the issue of missing files. CHANGES IN VERSION 0.99.6 ------------------------- o add ATAC plots. CHANGES IN VERSION 0.99.5 ------------------------- o Update R version dependency from 4.2.0 to 4.3.0 o remove 'CellChat', 'monocle3' and 'SeuratWrappers'. o re-organize the files in extdata to script and add documentation. o remove the `eval=FALSE` in vignettes and add `publish_folder` to scripts. o change the parameter of `cat` to `category` for `helper1` function. o remove `suppressWarnings/Messages`. o re-format the code style to fit 80 line width and 4 spaces for line indents. o add function to save ATAC peaks. CHANGES IN VERSION 0.99.4 ------------------------- o Update documentation. CHANGES IN VERSION 0.99.3 ------------------------- o Fix the heatmap donwload button. CHANGES IN VERSION 0.99.2 ------------------------- o Fix multiple notes. CHANGES IN VERSION 0.99.1 ------------------------- o Prepare for release.