NEWS

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scRNAseqApp 1.13.8

• Fix multiple element that not work in dark mode.

scRNAseqApp 1.13.7

• Add dark mode switch.

scRNAseqApp 1.13.6

• Expose the database folder as a parameter.

scRNAseqApp 1.13.5

• Change some files default path.

scRNAseqApp 1.13.4

• Add Z-axis.

scRNAseqApp 1.13.3

• Replace size with linewidth for geom_segment.

scRNAseqApp 1.13.2

• Add module privilege.

scRNAseqApp 1.13.1

• Fix the bug if variable genes for seurat object not found.

scRNAseqApp 1.11.26

• Add datasets available date.

scRNAseqApp 1.11.25

• Add search link for species.

scRNAseqApp 1.11.24

• Add 'download' button for webstats.

scRNAseqApp 1.11.23

• Add 'add' and 'delete' method for lasso.

scRNAseqApp 1.11.22

• Add desity plot for sunburst and deconvolution.

scRNAseqApp 1.11.21

• Fix the issue for idconv.

scRNAseqApp 1.11.20

• Add cell deconvolution plot.

scRNAseqApp 1.11.19

• Fix a bug in molecule plot for discrete_scale.

scRNAseqApp 1.11.17

• Using coord_cartesian but not xlim/ylim.

scRNAseqApp 1.11.16

• Add molecule module.

scRNAseqApp 1.11.15

• Fix the bugs in database links.

scRNAseqApp 1.11.14

• Add pan controler and resizable divider.

scRNAseqApp 1.11.13

• fix a bug for double click events in the user mode.

scRNAseqApp 1.11.12

• save cell segmentation for Seurat object.

scRNAseqApp 1.11.11

• add help function addCellBorders, addCellLinks and addBackgroundImage.

scRNAseqApp 1.11.10

• add background plot.

scRNAseqApp 1.11.9

• add cell segmentaion plot.

scRNAseqApp 1.11.8

• remove the force gene symbol table update.

scRNAseqApp 1.11.7

• fix the bug when subset the cells by percentage.

scRNAseqApp 1.11.6

• Add xlim and ylim for cellinfo and gene exprs plot give the possibility of cross dataset comparison.

scRNAseqApp 1.11.5

• replace 'size' by 'linewidth' for element_line in theme.

scRNAseqApp 1.11.4

• Keep the height controler for interactive plot in explorer.
• Add perentage filter for cell info plot.

scRNAseqApp 1.11.3

• Add apply lasso selection for explorer.

scRNAseqApp 1.11.2

• Add group B for reduction in explorer.

scRNAseqApp 1.11.1

• Add download function for lasso.

scRNAseqApp 1.9.26

• Fix the bug by sanitize the file names when load ATAC track.

scRNAseqApp 1.9.25

• add sum,max to plot type of Sunburst plot panel.

scRNAseqApp 1.9.24

• Add zoom in for plot.

scRNAseqApp 1.9.23

• Fix a bug for file accessibility check.

scRNAseqApp 1.9.22

• Add more color themes

scRNAseqApp 1.9.21

• support for dark mode

scRNAseqApp 1.9.20

• Add support for config.dcf file.

scRNAseqApp 1.9.19

• Add close and delete button for issues.

scRNAseqApp 1.9.18

• Update css for issues.

scRNAseqApp 1.9.17

• Add css for issues.

scRNAseqApp 1.9.16

• Add markdown support for issues.

scRNAseqApp 1.9.15

• Add edit and reply button for issues.

scRNAseqApp 1.9.14

• Fix the test when there is old files in the tmpfolder.

scRNAseqApp 1.9.13

• Handle the file accessibility issue.

scRNAseqApp 1.9.12

• Fix the bug if the script.js does not update.

scRNAseqApp 1.9.11

• Add issues tab.

scRNAseqApp 1.9.10

• Update the homepage to include datasets information.

scRNAseqApp 1.9.9

• Update the unit test.

scRNAseqApp 1.9.8

• Filter cells by a range of value.

scRNAseqApp 1.9.7

• Allow single gene heatmap plot.

scRNAseqApp 1.9.6

• Add progress bar for atac signal plot.

scRNAseqApp 1.9.3

• Adjust the atac peak links plot space.

scRNAseqApp 1.9.2

• Add edge links.

scRNAseqApp 1.9.1

• Fix the issue for ATAC track plot if there is no 'type' in peak annotation and no 'score' in links.

scRNAseqApp 1.7.14

• Add function extractFragmentNameMapList.

scRNAseqApp 1.7.13

• Add search for token.

scRNAseqApp 1.7.12

• Fix the token issue.

scRNAseqApp 1.7.11

• Fix the issue if the data list is not updated for the main page.

scRNAseqApp 1.7.10

• Fix multiple typos.

scRNAseqApp 1.7.9

• Update the footnote.

scRNAseqApp 1.7.8

• Remove the import of X11Fonts.

scRNAseqApp 1.7.7

• Update email address.

scRNAseqApp 1.7.6

• Add fragmentNameMap to createDataset.
• Add fragmentNameMap to createDataset.

scRNAseqApp 1.7.5

• Optimize read and save ATAC peak matrix.

scRNAseqApp 1.7.4

• Add module ExplorerAcc.

scRNAseqApp 1.7.3

• check parameters before creating dataset.

scRNAseqApp 1.7.2

• add binSize parameter for atac bigwig files.

scRNAseqApp 1.7.1

• fix the bug if no signals for atac coverage and invalid filenames.

scRNAseqApp 1.5.22

• add warning message to log file when the atac bigwig files are not available.

scRNAseqApp 1.5.21

• fix a bug that counter table is not available.

scRNAseqApp 1.5.20

• Add csv format for figure data download.

scRNAseqApp 1.5.19

• Try to handle the error 'Timeout was reached: [www.ncbi.nlm.nih.gov] SSL/TLS connection timeout'.

scRNAseqApp 1.5.18

• add protection of column sampleID in cell info editor funcitons.

scRNAseqApp 1.5.17

• Error handle if metadata contains '|'.
• add cell info editor funcitons.

scRNAseqApp 1.5.16

• add more download format.

scRNAseqApp 1.5.15

• fix the low resolution of the plot.

scRNAseqApp 1.5.14

• fix the dotplot download issue.

scRNAseqApp 1.5.13

• add detailed fontsize and font family control.
• change the dotplot from ggplot2 to complexheatmap.

scRNAseqApp 1.5.12

• order the stacked violin plots by input order.

scRNAseqApp 1.5.11

• add reorder function for splitBy for violin plots.

scRNAseqApp 1.5.10

• add color picker.
• add splitBy for violin plots.
• fix the issue that refresh explorer will lost the subset info.

scRNAseqApp 1.5.9

• add help video playlist.

scRNAseqApp 1.5.8

• add functionality to allow different labels for cell info.
• allow subset groups for explorer.

scRNAseqApp 1.5.7

• fix the issue of reload everything when edit the cell info.

scRNAseqApp 1.5.6

• Editable cell info during login mode.
• Hiden the cells when check the hidden box.

scRNAseqApp 1.5.5

• Response to the download width and height.

scRNAseqApp 1.5.4

• Access tab via query string.

scRNAseqApp 1.5.3

• Access data via data title.

scRNAseqApp 1.5.2

• Add favicon.

scRNAseqApp 1.5.1

• Fix the unique vistor counter.

scRNAseqApp 1.3.25

• Fix the abstract issue for edit module.

scRNAseqApp 1.3.24

• Update the description.

scRNAseqApp 1.3.23

• Add a hyperlink to package URL at footer.

scRNAseqApp 1.3.22

• Fix the duplicated rownames.

scRNAseqApp 1.3.21

• Add search button in the home page.

scRNAseqApp 1.3.20

• Change the default waffle plot group to celltype.

scRNAseqApp 1.3.19

• Update abstract in the admin edit tab.

scRNAseqApp 1.3.18

• Add abstract parameter for createAppConfig

scRNAseqApp 1.3.17

• Fix the issue if no ip location information available when update from the older version.
• add the possibility of the feature names to replace the rownames.

scRNAseqApp 1.3.16

• Fix the missmatch UI and ID.

scRNAseqApp 1.3.15

• Fix the no id column issue when update the database.

scRNAseqApp 1.3.14

• Update the maxOptions from 6 to 50.

scRNAseqApp 1.3.13

• Add groupby parameter for correlation for proportion plot.

scRNAseqApp 1.3.12

• Add correlation for proportion plot.

scRNAseqApp 1.3.11

• Add Wilcoxon test for violin plot.

scRNAseqApp 1.3.10

• Add Chisq test for proportion.

scRNAseqApp 1.3.9

• Fix some typos.

scRNAseqApp 1.3.8

• Change dependence from hdf5r to rhdf5.

scRNAseqApp 1.3.7

• Fix the wrong downloader handler in downloader module.

scRNAseqApp 1.3.6

• Add downloader module.

scRNAseqApp 1.3.5

• Add gene name map to sql database.

scRNAseqApp 1.3.4

• Fix the issue of missing stats for cell numbers.

scRNAseqApp 1.3.3

• Add user visit info and gene symbols into the sql database.

scRNAseqApp 1.3.2

• Add dataset configuration into the sql database.

scRNAseqApp 1.3.1

• Make it compatable with SeuratObject V5.

scRNAseqApp 1.1.10

• Fix the download button for the explorer module.

scRNAseqApp 1.1.9

• Fix the repeat retreive for reference by createAppConfig.

scRNAseqApp 1.1.8

• Change the filepath for credential file.

scRNAseqApp 1.1.7

• Fix the bug in scInit for datafolder.

scRNAseqApp 1.1.6

• Fix the download button which download the fixed values.
• Add multiple subset buttons.

scRNAseqApp 1.1.5

• List the available datasets by users privilege.

scRNAseqApp 1.1.4

• Fix the bug if the data is removed where user is explorering.

scRNAseqApp 1.1.3

• Fix the bug introduced by changing actionBution to checkboxInput for modBubbleHeatmap.

scRNAseqApp 1.1.2

• Add multiple layer of violin plot
• Add sample order controls for stats plot

scRNAseqApp 1.1.1

• Fix the bug that 'coverage' function is not imported.

scRNAseqApp 0.99.27

• Fix the subtitles for scATACseq data.

scRNAseqApp 0.99.25

• Fix a typo when fixing the chromsome name style for scATACseq data.

scRNAseqApp 0.99.24

• Add tracks for scATACseq data.

scRNAseqApp 0.99.23

• Add title for ATAC plot buttons.

scRNAseqApp 0.99.22

• Fix the issue if there is no reference.

scRNAseqApp 0.99.21

• Fix the typo for 'createDataset' function.

scRNAseqApp 0.99.20

• Add zoom in and out for atac track plots.

scRNAseqApp 0.99.19

• Update the atac track plots.

scRNAseqApp 0.99.18

• Simplify the about module.

scRNAseqApp 0.99.17

• Update documentation for cellgene VIP.

scRNAseqApp 0.99.16

• fix the bug for cell index for waffleplot.

scRNAseqApp 0.99.15

• fix the bug if no reference can be retrieved.

scRNAseqApp 0.99.14

• fix the bug if no markers can be detected.

scRNAseqApp 0.99.13

• remove aes_string.

scRNAseqApp 0.99.12

• fix the dropdown names issue.

scRNAseqApp 0.99.11

• add check/uncheck all to subset cells.

scRNAseqApp 0.99.10

• fix the multiple loading.

scRNAseqApp 0.99.9

• fix the long table in vignette.

scRNAseqApp 0.99.8

• add app_path to app to fix the issue of missing files.

scRNAseqApp 0.99.6

• add ATAC plots.

scRNAseqApp 0.99.5

• Update R version dependency from 4.2.0 to 4.3.0
• remove 'CellChat', 'monocle3' and 'SeuratWrappers'.
• re-organize the files in extdata to script and add documentation.
• remove the 'eval=FALSE' in vignettes and add 'publish_folder' to scripts.
• change the parameter of 'cat' to 'category' for 'helper1' function.
• remove 'suppressWarnings/Messages'.
• re-format the code style to fit 80 line width and 4 spaces for line indents.
• add function to save ATAC peaks.

scRNAseqApp 0.99.4

• Update documentation.

scRNAseqApp 0.99.3

• Fix the heatmap donwload button.

scRNAseqApp 0.99.2

• Fix multiple notes.

scRNAseqApp 0.99.1

• Prepare for release.