samuel-marsh/scCustomize issues and pull requests

#103 - Option to edit Features names in Clustered_DotPlot => italicized

Issue - State: closed - Opened by BaptLabRight over 1 year ago - 2 comments

#102 - Error knitting Rmarkdown

Issue - State: closed - Opened by williamsdrake over 1 year ago - 2 comments

#101 - Seurat V5 Compatibility Update (Dev Note/Plan)

Issue - State: closed - Opened by samuel-marsh over 1 year ago - 14 comments
Labels: bug, documentation, enhancement, New Feature, Vignette Related, Not Working As Intended, more-info-needed, Release Prep

#100 - some functions can not be used when installed seurat v5

Issue - State: closed - Opened by caodudu over 1 year ago - 2 comments

#99 - Cannot Read h5 file after starsolo+cellbender

Issue - State: closed - Opened by ayyildizd over 1 year ago - 13 comments

#98 - Reorder clustered columns in Clustered_DotPlot()

Issue - State: closed - Opened by ms-gx over 1 year ago - 2 comments
Labels: enhancement

#97 - FeaturePlot_scCustom fails to plot DR loadings

Issue - State: closed - Opened by samuel-marsh over 1 year ago - 1 comment
Labels: bug

#96 - Adjust size x-axis labels (col_label_size)

Issue - State: closed - Opened by massonix over 1 year ago - 6 comments
Labels: enhancement

#95 - Additional features to implement

Issue - State: closed - Opened by kasumaz over 1 year ago - 3 comments

#94 - Legend in FeaturePlot_scCustom

Issue - State: closed - Opened by bio-visualisation over 1 year ago - 2 comments

#93 - clustered dot plot hierarchical clustering differs from seurat dotplot hierarchical clustering

Issue - State: closed - Opened by sakatash over 1 year ago - 3 comments
Labels: Not Working As Intended

#92 - CellBender dual assay object

Issue - State: closed - Opened by giorgiatosoni over 1 year ago - 4 comments

#91 - Parameter 'raster' of function 'QC_Plots_Feature' is not passed to 'VlnPlot'

Issue - State: closed - Opened by YukuanHuang over 1 year ago - 3 comments
Labels: bug

#90 - State Abundance Plotting

Issue - State: open - Opened by samuel-marsh over 1 year ago - 1 comment
Labels: New Feature

#89 - Add aspect_ratio parameter

Issue - State: closed - Opened by samuel-marsh over 1 year ago

#88 - adding metadata after reading multipal files

Issue - State: closed - Opened by amoyguang1 over 1 year ago - 3 comments

#87 - adding SpatialFeaturePlot function

Issue - State: closed - Opened by psecekartal over 1 year ago - 7 comments
Labels: New Feature

#86 - Release 1.1.1

Pull Request - State: closed - Opened by samuel-marsh over 1 year ago

#85 - Release 1.1.1 Prep

Issue - State: closed - Opened by samuel-marsh over 1 year ago - 1 comment
Labels: documentation, Vignette Related, Release Prep

#84 - 90 degree x label

Issue - State: closed - Opened by AltayYuzeir over 1 year ago - 3 comments
Labels: enhancement

#83 - FIX: Some scCustomize cli-based warnings are being ignored accidentally.

Issue - State: closed - Opened by samuel-marsh over 1 year ago - 1 comment
Labels: bug, Not Working As Intended

#82 - Finish error/warning to cli/rlang framework

Issue - State: closed - Opened by samuel-marsh almost 2 years ago
Labels: enhancement, Release Prep

#81 - Release 1.1.0

Pull Request - State: closed - Opened by samuel-marsh almost 2 years ago - 1 comment

#80 - Labeling clusters with FeaturePlot_scCustom in v1.0

Issue - State: closed - Opened by jeremynkay almost 2 years ago - 2 comments

#79 - how to get the defualt color in dimplot

Issue - State: closed - Opened by littleju777 almost 2 years ago

#78 - Release 1.1.0

Pull Request - State: closed - Opened by samuel-marsh almost 2 years ago

#77 - Prep 1.1.0 Release

Issue - State: closed - Opened by samuel-marsh almost 2 years ago - 1 comment
Labels: enhancement, Vignette Related, Release Prep

#76 - Error in CreateAssayObject() from cellbender to seurat

Issue - State: closed - Opened by Jiayi-Zheng almost 2 years ago - 3 comments

#75 - Prep v1.0.2 Release

Issue - State: closed - Opened by samuel-marsh almost 2 years ago - 3 comments
Labels: Release Prep

#74 - Add_Mito_Ribo error

Issue - State: closed - Opened by giorgiatosoni almost 2 years ago - 12 comments

#73 - Merge for 1.0.1 Release

Pull Request - State: closed - Opened by samuel-marsh almost 2 years ago

#72 - Merge_Seurat_List memory allocation error

Issue - State: closed - Opened by wvictor14 almost 2 years ago - 3 comments

#71 - Prep 1.0.1 Release

Issue - State: closed - Opened by samuel-marsh almost 2 years ago - 1 comment
Labels: documentation, enhancement, New Feature, Vignette Related, Release Prep

#70 - CellBender genes removed?

Issue - State: closed - Opened by giorgiatosoni almost 2 years ago - 4 comments
Labels: enhancement, New Feature

#69 - Flip clustered dotplot

Issue - State: closed - Opened by france-hub almost 2 years ago - 5 comments
Labels: enhancement

#68 - Merge for v1.0.0 Release

Pull Request - State: closed - Opened by samuel-marsh almost 2 years ago

#67 - Adding NoLegend() option

Issue - State: closed - Opened by jjo12 almost 2 years ago - 5 comments

#66 - Error in Split_FeatureScatter

Issue - State: closed - Opened by CoderMatthias almost 2 years ago - 2 comments

#65 - Same scale bar for multiple features

Issue - State: closed - Opened by jmrussell almost 2 years ago - 1 comment

#64 - Featureplot not plotting if one of the variables is missing from the seurat object

Issue - State: closed - Opened by Prathyusha-konda almost 2 years ago - 6 comments
Labels: bug

#63 - Stacked_VlnPlot + Legend

Issue - State: closed - Opened by teresa-swift almost 2 years ago - 1 comment

#62 - v1.0.0 Release Prep

Issue - State: closed - Opened by samuel-marsh about 2 years ago
Labels: documentation, enhancement, New Feature, Vignette Related, Release Prep

#61 - Fix Matrix In read functions from Seurat

Issue - State: closed - Opened by samuel-marsh about 2 years ago - 1 comment

#60 - Allow feature names to be plotted in secondary Y axis instead of in the color legend

Issue - State: closed - Opened by gabrielnegreira about 2 years ago - 3 comments
Labels: enhancement

#59 - Check replace accessors with pluck

Issue - State: closed - Opened by samuel-marsh about 2 years ago - 1 comment
Labels: enhancement

#58 - Clustered_DotPlot() : reorganize cluster order

Issue - State: closed - Opened by eadaui about 2 years ago

#57 - meta_sample_list_test' not found

Issue - State: closed - Opened by dacheampong about 2 years ago - 2 comments
Labels: bug

#56 - Are cell numbers normalized?

Issue - State: closed - Opened by singcell about 2 years ago - 2 comments

#55 - Any way to change legend order?

Issue - State: closed - Opened by SimoniMD about 2 years ago - 1 comment

#54 - Add Read h5 for CellBender v3 Files

Issue - State: closed - Opened by samuel-marsh about 2 years ago
Labels: New Feature, Vignette Related

#53 - Plot_Density_Custom custom_palette option only applies the custom palette to last plot if passed multiple genes

Issue - State: closed - Opened by jdparker101 about 2 years ago - 2 comments

#52 - move ggrastr to Suggests

Issue - State: closed - Opened by cstubben about 2 years ago - 4 comments

#51 - Fix LIGER mito/ribo naming

Issue - State: closed - Opened by samuel-marsh about 2 years ago
Labels: bug, Not Working As Intended

#50 - Add Cell Complexity

Issue - State: closed - Opened by samuel-marsh about 2 years ago
Labels: New Feature, Vignette Related

#49 - Error in scCustomize_Palette(num_groups = group_by_length, ggplot_default_colors = ggplot_default_colors, : object 'color_seed' not found

Issue - State: closed - Opened by eadaui about 2 years ago - 6 comments
Labels: bug, Not Working As Intended

#48 - Color legends for VlnPlot and Stacked_VlnPlot

Issue - State: closed - Opened by nikofleischer about 2 years ago - 5 comments

#47 - Are the barplots applicable to expression features split by groupings/condition?

Issue - State: closed - Opened by levinhein over 2 years ago - 3 comments

#46 - Add new features delim read functions

Issue - State: closed - Opened by samuel-marsh over 2 years ago - 1 comment
Labels: enhancement

#45 - Add LIGER Variable Features (all datasets)

Issue - State: closed - Opened by samuel-marsh over 2 years ago - 1 comment
Labels: New Feature

#44 - DotPlot_scCustom do not plot meta data variables

Issue - State: closed - Opened by saeedfc over 2 years ago - 7 comments

#43 - Move progress bars to cli framework

Issue - State: open - Opened by samuel-marsh over 2 years ago - 1 comment
Labels: enhancement, Release Prep

#42 - Fix Double raster error messages VlnPlot

Issue - State: closed - Opened by samuel-marsh over 2 years ago - 1 comment
Labels: Not Working As Intended

#41 - Check website reference table of contents

Issue - State: closed - Opened by samuel-marsh over 2 years ago - 1 comment
Labels: Vignette Related

#40 - Make Figure DimPlot

Issue - State: closed - Opened by samuel-marsh over 2 years ago - 1 comment
Labels: enhancement, New Feature, Vignette Related

#38 - Check plot returns

Issue - State: closed - Opened by samuel-marsh over 2 years ago - 1 comment
Labels: enhancement

#37 - Fixing levels of grouping variables when splitting DimPlots

Issue - State: closed - Opened by nikofleischer over 2 years ago - 7 comments
Labels: bug, Not Working As Intended

#36 - Stacked_VlnPlot change labels

Issue - State: closed - Opened by nikofleischer over 2 years ago - 3 comments

#35 - Clustered_DotPlot: Error in ComplexHeatmap::Legend

Issue - State: closed - Opened by Sophia409 over 2 years ago - 4 comments
Labels: bug

#34 - `*_Highlight_Plot` enhancements

Issue - State: closed - Opened by samuel-marsh over 2 years ago
Labels: documentation, enhancement

#33 - Check cli/rlang replacements

Issue - State: closed - Opened by samuel-marsh over 2 years ago - 1 comment
Labels: documentation, enhancement

#32 - control border thickness of Stacked_VlnPlot

Issue - State: closed - Opened by massonix over 2 years ago - 9 comments
Labels: enhancement, Not Working As Intended

#31 - setting combine = FALSE in FeaturePlot_scCustomize() returns NULL

Issue - State: closed - Opened by nikofleischer over 2 years ago - 6 comments

#30 - functions appear to not follow the same coloring scheme

Issue - State: closed - Opened by osmansharifi over 2 years ago - 9 comments
Labels: bug

#29 - Unable to override default identity colors in Clustered Dotplot

Issue - State: closed - Opened by SimoniMD over 2 years ago - 11 comments
Labels: bug

#28 - Integration of different species datasets

Issue - State: closed - Opened by giorgiatosoni over 2 years ago - 9 comments

#27 - Clustered_DotPlot cannot add another layer to change x-axis ticks

Issue - State: closed - Opened by Ssl2Translocase over 2 years ago - 4 comments
Labels: enhancement

#26 - SingleCellExperiment support

Issue - State: closed - Opened by MarcElosua over 2 years ago - 1 comment

#25 - Depend on colorway >= 0.2.0

Pull Request - State: closed - Opened by mojaveazure over 2 years ago - 1 comment

#24 - Fix QC Seurat VlnPlots

Issue - State: closed - Opened by samuel-marsh over 2 years ago
Labels: bug

#23 - Test Seurat 4.1.0 Update

Issue - State: closed - Opened by samuel-marsh over 2 years ago

#22 - Add CNAME

Pull Request - State: closed - Opened by samuel-marsh over 2 years ago

#21 - Adding Alpha/Transparency to FeaturePlot

Issue - State: closed - Opened by jkaiser87 over 2 years ago - 6 comments
Labels: enhancement

#20 - Merge for v0.7.0 Release

Pull Request - State: closed - Opened by samuel-marsh over 2 years ago

#19 - Clustered_DotPlot Error: number of cluster centres must lie between 1 and nrow(x)

Issue - State: closed - Opened by crazyhottommy over 2 years ago - 15 comments
Labels: bug

#18 - Clustered Dotplot

Issue - State: closed - Opened by samuel-marsh almost 3 years ago - 9 comments
Labels: enhancement, Vignette Related

#17 - Add to Meta Data slot

Issue - State: closed - Opened by samuel-marsh almost 3 years ago
Labels: New Feature, Release Prep

#16 - Move to `abort()` framework when rlang 1.0.0 releases

Issue - State: closed - Opened by samuel-marsh almost 3 years ago - 2 comments
Labels: documentation, enhancement

#15 - Add raster support to `StackedVlnPlot`

Issue - State: closed - Opened by samuel-marsh almost 3 years ago - 1 comment
Labels: enhancement

#14 - Merge for Version 0.6.3 Release

Pull Request - State: closed - Opened by samuel-marsh almost 3 years ago

#13 - Create `VlnPlot_scCustom` Function

Issue - State: closed - Opened by samuel-marsh almost 3 years ago - 2 comments
Labels: New Feature, Vignette Related

#12 - import DefaultDimReduc from SeuratObject

Pull Request - State: closed - Opened by crazyhottommy almost 3 years ago - 6 comments

#11 - Add URL

Pull Request - State: closed - Opened by maelle almost 3 years ago - 4 comments

#10 - Version 0.6.2 Release

Pull Request - State: closed - Opened by samuel-marsh almost 3 years ago

#8 - Fix potential barcode name collisions when providing prefix

Issue - State: closed - Opened by samuel-marsh almost 3 years ago - 1 comment
Labels: bug, Not Working As Intended

#5 - Add VlnPlot `raster` as default parameter

Issue - State: closed - Opened by samuel-marsh almost 3 years ago - 1 comment
Labels: enhancement

#4 - Add Features Mito/Ribo Functions

Issue - State: closed - Opened by samuel-marsh almost 3 years ago
Labels: enhancement

#3 - Added features for `Percent_Expressing`

Issue - State: open - Opened by samuel-marsh almost 3 years ago - 2 comments
Labels: enhancement

#2 - Progress Bars for Parallel Read Functions

Issue - State: closed - Opened by samuel-marsh almost 3 years ago
Labels: bug, enhancement, Not Working As Intended, Help Wanted

#1 - New Features/Enhancements in Development

Issue - State: open - Opened by samuel-marsh about 3 years ago
Labels: enhancement, New Feature

GitHub / samuel-marsh/scCustomize issues and pull requests