i2dash.scRNAseq merge requestshttps://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests2020-11-06T15:14:54Zhttps://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/77Extend readme2020-11-06T15:14:54Zarsenij.ustjanzewExtend readmehttps://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/76Extend readme2020-11-05T16:06:27Zarsenij.ustjanzewExtend readmehttps://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/75Update README.md2020-06-23T13:25:29Zarsenij.ustjanzewUpdate README.mdhttps://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/63Readme2020-06-16T11:04:45Zarsenij.ustjanzewReadmeThis branch contains 5 vignettes:
- use-case 1-3; Documentation (overview of all components and pages); guide for developer
also a page created with the pkgdown packageThis branch contains 5 vignettes:
- use-case 1-3; Documentation (overview of all components and pages); guide for developer
also a page created with the pkgdown packagehttps://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/62Update DESCRIPTION2020-06-10T11:46:44Zarsenij.ustjanzewUpdate DESCRIPTIONhttps://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/27WIP: Documentation updates2020-06-09T11:55:24Zjens.preussnerWIP: Documentation updatesThis MR collects several updates in documentation (wording, parameter names, etc) in order to harmonize across the entire package.This MR collects several updates in documentation (wording, parameter names, etc) in order to harmonize across the entire package.https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/56linking of components2020-05-07T07:57:06Zarsenij.ustjanzewlinking of componentsImplementation of linking between scatterplot and existing components. See https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/merge_requests/30 for further details.Implementation of linking between scatterplot and existing components. See https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/merge_requests/30 for further details.https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/33Bubbleplot2020-05-07T07:15:36Zarsenij.ustjanzewBubbleplotThe code used in the vignette for developer to implement a bubbleplot as component.The code used in the vignette for developer to implement a bubbleplot as component.https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/47Feature selection page2020-05-04T11:10:06Zarsenij.ustjanzewFeature selection pageImplementation of a page to quantify per-gene variation and explore the threshold on the metric of variation to get the desired set of highly variable features.
Creates a page with a scatterplot of the variance of log-expression against...Implementation of a page to quantify per-gene variation and explore the threshold on the metric of variation to get the desired set of highly variable features.
Creates a page with a scatterplot of the variance of log-expression against the mean log-expression and a table with features and their metrics of variation. With shiny inputs you can color highlight the hvgs in dependency to the proportion and minimal threshold of the relevant variation metric. Also you can download the selcted hvgs or the entire variation metrics table.https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/74package check2020-05-04T10:55:37Zarsenij.ustjanzewpackage checkresolved errors notes and most warnings of devtools::check()resolved errors notes and most warnings of devtools::check()https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/73Heatmap download2020-05-04T08:44:38Zarsenij.ustjanzewHeatmap downloadhttps://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/72Description "subset_row" for feature-comparison-page2020-03-30T16:04:31Zarsenij.ustjanzewDescription "subset_row" for feature-comparison-pageadded parameter description "subset_row" for feature-comparison-pageadded parameter description "subset_row" for feature-comparison-pagehttps://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/70Fixed summarize_metadata2020-03-26T09:22:59Zarsenij.ustjanzewFixed summarize_metadatahttps://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/71Important fix of feature_expression_page!2020-03-26T09:22:34Zarsenij.ustjanzewImportant fix of feature_expression_page!https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/69Cleanly added comparison page2020-03-09T15:18:31Zjens.preussnerCleanly added comparison pageClean add of work from !61 that was reverted in !68Clean add of work from !61 that was reverted in !68https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/68Revert "Merge branch 'dimred_comparison_page' into 'master'"2020-03-09T15:18:27Zjens.preussnerRevert "Merge branch 'dimred_comparison_page' into 'master'"This reverts merge request !61This reverts merge request !61https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/61fusion of umap and tsne in one comparison page.2020-03-09T15:18:26Zarsenij.ustjanzewfusion of umap and tsne in one comparison page.add_dimred_comparison_page()add_dimred_comparison_page()https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/67summarize_discarded2020-03-06T08:44:10Zarsenij.ustjanzewsummarize_discardedimplemented component with table containing statistics of discarded and kept samples per experimental factorimplemented component with table containing statistics of discarded and kept samples per experimental factorhttps://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/46Summarize functions2020-03-06T08:44:04Zarsenij.ustjanzewSummarize functionsA small change of the function parameters to make it easier to understand, which parameter are required.A small change of the function parameters to make it easier to understand, which parameter are required.https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq/-/merge_requests/65Colormap for the feature_expression_page2020-03-03T11:50:40Zarsenij.ustjanzewColormap for the feature_expression_pageAdded the missing colormaps functionalityAdded the missing colormaps functionality