samuel-marsh/scCustomize issues and pull requests

#116 - Split_FeatureScatter missing correlation output

Issue - State: closed - Opened by skim245 over 1 year ago - 3 comments

#115 - Read_Metrics_10X error

Issue - State: closed - Opened by rhart604 over 1 year ago - 16 comments
Labels: bug

#114 - "Error in x$exists(name) : HDF5-API Errors" running "Read_CellBender_h5_Mat"

Issue - State: closed - Opened by sahanda66 over 1 year ago - 5 comments
Labels: bug

#113 - Question: what should I provide to add.cell.ids in Merge_Seurat_List()?

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

#112 - Release/1.1.2

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

#111 - Vignettes not properly displaying pre-rendered images & other errors

Issue - State: closed - Opened by samuel-marsh over 1 year ago
Labels: bug, Vignette Related

#110 - Package is not available for R version 4.2.1

Issue - State: closed - Opened by kboufea over 1 year ago - 7 comments

#109 - New Violin Plot Function (analogous to scanpy: `sc.pl.stacked_violin` with identity on y axis

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

#108 - Bring NoLegend, NoAxes inside of Iterative Plotting Functions

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

#107 - Release 1.1.2

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

#106 - Clustered_DotPlot clustering option for row/column

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

#105 - Depicting the same number of cells per condition/orig.ident in DimPlot_scCustom

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

#104 - Merge_Sparse_Data_All with multimodal sparse matrices

Issue - State: closed - Opened by pankomah over 1 year ago - 5 comments

#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 almost 2 years ago - 4 comments

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

Issue - State: closed - Opened by YukuanHuang almost 2 years ago - 3 comments
Labels: bug

#90 - State Abundance Plotting

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

#89 - Add aspect_ratio parameter

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

#88 - adding metadata after reading multipal files

Issue - State: closed - Opened by amoyguang1 almost 2 years ago - 3 comments

#87 - adding SpatialFeaturePlot function

Issue - State: closed - Opened by psecekartal almost 2 years ago - 7 comments
Labels: New Feature

#86 - Release 1.1.1

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

#85 - Release 1.1.1 Prep

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

#84 - 90 degree x label

Issue - State: closed - Opened by AltayYuzeir almost 2 years ago - 3 comments
Labels: enhancement

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

Issue - State: closed - Opened by samuel-marsh almost 2 years 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 about 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 about 2 years ago - 3 comments

#75 - Prep v1.0.2 Release

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

#74 - Add_Mito_Ribo error

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

#73 - Merge for 1.0.1 Release

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

#72 - Merge_Seurat_List memory allocation error

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

#71 - Prep 1.0.1 Release

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

#70 - CellBender genes removed?

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

#69 - Flip clustered dotplot

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

#68 - Merge for v1.0.0 Release

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

#67 - Adding NoLegend() option

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

#66 - Error in Split_FeatureScatter

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

#65 - Same scale bar for multiple features

Issue - State: closed - Opened by jmrussell about 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 about 2 years ago - 6 comments
Labels: bug

#63 - Stacked_VlnPlot + Legend

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

#54 - Add Read h5 for CellBender v3 Files

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

#52 - move ggrastr to Suggests

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

#51 - Fix LIGER mito/ribo naming

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

#50 - Add Cell Complexity

Issue - State: closed - Opened by samuel-marsh over 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 over 2 years ago - 6 comments
Labels: bug, Not Working As Intended

GitHub / samuel-marsh/scCustomize issues and pull requests