GitLab

adjusted createImgMap() to only plot pathways with clickable links for which gene information are available (for the others the .pathways/*.png files will be plotted)

added -p flag to mkdir in the `mcdir()` function in order to create intermediate directories if required

added export of various count type data (raw, normalized, scaled, regressed); fixed clustering loop for the case when multiple PCs are selected

corrected output folder for the filtered count matrix; information for the selected PC are now additionally exported as a R object which can be visualized in the metrics_explorer app.

added option to set cell cycle markers gene list for the cell cycle correction; outliers are now removed if outlier information is available from the annotation data; Seurat quality metrics are only plotted once but with the set thresholds as horizontal lines; all meta data are exported as cell_infos.txt which serves as input for the metrics_explorer app

moved plotExplanatoryVariables() to the end of the script to be able to take cell cycle phase information into account; improved guess_annot_db() selection; cosmetics

replaced radioButton() by selectInput(); now all cluster information will be converted to factor and are also available to explore quality metrics per cluster

added additional gene information of top50 most abundant genes; gene information are exported if requested

added subsetting of countMatrix to ncol = 2000 if the input data contains more than 2000 cells; removed plotting of diffusion map and pseudo time; added PCA and its data export as R object

removed bsplus extras; fixed kable() table export by adding kable_styling(); removed calculation of mitochondrial genes (too specific for the individual data sets); total_counts and total_features take now all features into account; cosmetics

added code to source diffex_commons.R; added option to download gene information based on the count matrix rownames; cosmetics

replaced `library()` by `loadpack`; updated functions for the current scater version; added PCA based on quality metrices in order to detect outliers; added explanatory variables plot based on all input information in the design file; exports now information on gene name, description and coordinates if ensembl gene ids are provided in the count matrix; added code to copy the used script to the working directory and to export session information