samuel-marsh/scCustomize issues and pull requests

#215 - About the scCustomize package dependent package error

Issue - State: closed - Opened by PanSX-Dr 12 days ago - 4 comments

#214 - release/3.0.0 install issue

Issue - State: closed - Opened by aherman-umn 14 days ago - 1 comment

#213 - scCustomize generating empty plots

Issue - State: closed - Opened by rasing02 15 days ago - 10 comments

#212 - Bug fixes (Plot_Density_Custom and Plot_Density_Joint_Only drawing) ；Picture saving

Issue - State: closed - Opened by Roner2022 22 days ago - 1 comment

#212 - Bug fixes (Plot_Density_Custom and Plot_Density_Joint_Only drawing) ；Picture saving

Issue - State: closed - Opened by Roner2022 22 days ago - 1 comment

#211 - Option to change dot size in Clustered_DotPlot()?

Issue - State: closed - Opened by reyancoskun 27 days ago - 1 comment

#211 - Option to change dot size in Clustered_DotPlot()?

Issue - State: closed - Opened by reyancoskun 27 days ago - 1 comment

#210 - Iterate_FeaturePlot_scCustom error

Issue - State: closed - Opened by mph270 28 days ago - 3 comments

#209 - Updated_HGNC_Symbols tries to download from non-existent site.

Issue - State: closed - Opened by Abiologist about 1 month ago - 1 comment

#208 - QC_Plots_Mito for merged dual cellbender-cellranger seurat object does not match that for individual cellbender-cellranger seurat object

Issue - State: closed - Opened by mph270 about 1 month ago - 7 comments

#207 - as.anndata raises error in which(): argument to which () is not logical

Issue - State: closed - Opened by tjm-sci about 2 months ago - 3 comments

#206 - as.anndata error with which(single_val_columns)) argument to 'which' is not logical

Issue - State: closed - Opened by brainfo about 2 months ago - 3 comments

#205 - Error in .subset2(x, i, exact = exact) : subscript out of bounds

Issue - State: closed - Opened by Runzhi819 2 months ago - 1 comment

#204 - Release 3.0.0

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

#203 - Release/3.0.0

Pull Request - State: open - Opened by samuel-marsh 2 months ago

#202 - Updated_HGNC_Symbols using mouse genes

Issue - State: closed - Opened by siv2108 3 months ago - 2 comments
Labels: enhancement, New Feature

#201 - "split.by" option in Cluster Highlight Plot caused error

Issue - State: closed - Opened by jasonleongbio 3 months ago - 3 comments

#200 - Add new parameter in DimPlot_scCustom to bury a group, or add a new parameter in Meta_Highlight_Plot() to allow the buried cells to appear in legend

Issue - State: closed - Opened by CroixJeremy2 3 months ago - 2 comments

#199 - request pass parameters to ComplexHeatmap::Heatmap

Issue - State: closed - Opened by johnminglu 3 months ago - 9 comments
Labels: enhancement, more-info-needed

#198 - "reduction" argument missing on "Cluster Highlight Plot" man page

Issue - State: closed - Opened by jasonleongbio 3 months ago - 1 comment

#197 - unused argument (alpha = alpha_exp) erro in FeaturePlot_scCustom

Issue - State: closed - Opened by shanshancode 4 months ago - 4 comments
Labels: bug, more-info-needed

#196 - Clarification regarding `exp_value_type = "scaled"` in `scCustomize::Clustered_DotPlot`

Issue - State: closed - Opened by denvercal1234GitHub 4 months ago - 1 comment

#195 - When converting from Seurat RDS to anndata h5ad, gene names are lost.

Issue - State: closed - Opened by joshuak94 4 months ago - 9 comments
Labels: bug, Not Working As Intended

#194 - Adjusting font size with theme() does not work with figure_plot = TRUE

Issue - State: open - Opened by wendelljpereira 4 months ago - 1 comment

#193 - ! Column name `barcodes` must not be duplicated.

Issue - State: closed - Opened by Flu09 4 months ago - 2 comments

#192 - Setting a scale/limit for `scCustomize::Plot_Density_Custom`?

Issue - State: closed - Opened by denvercal1234GitHub 4 months ago - 6 comments

#191 - Solution around Warning: Renaming features in v3/v4 assays is not supported following `scCustomize::Updated_HGNC_Symbols`

Issue - State: closed - Opened by denvercal1234GitHub 4 months ago - 2 comments

#190 - Due to error in Nebulosa package and ggplot2 v3.5.0

Issue - State: closed - Opened by XIANZHE-LI 4 months ago - 2 comments

#189 - ensure `na_ok` is adhered to in `Add_Sample_Meta`

Pull Request - State: closed - Opened by fbearoff 4 months ago - 1 comment

#188 - conversion to anndata

Issue - State: closed - Opened by Flu09 6 months ago - 17 comments
Labels: more-info-needed

#187 - Error Merge

Issue - State: closed - Opened by eblchen 6 months ago - 11 comments

#186 - Enable `Add_Cell_QC_Metrics()` to Support ENSEMBL IDs for "IEG" and "MSig_DB"

Issue - State: closed - Opened by JuanTejedor 6 months ago - 2 comments
Labels: enhancement

#185 - Plots not printing

Issue - State: closed - Opened by hcjarnagin 7 months ago - 2 comments
Labels: more-info-needed

#184 - Add_Mito_Ribo multiple species

Issue - State: closed - Opened by rhart604 7 months ago - 3 comments
Labels: enhancement

#183 - MAD_stats mad_num variable doesn't change value

Issue - State: closed - Opened by chloetu-dfci 7 months ago - 5 comments
Labels: bug

#182 - Set different color palettes to be used for different assays in FeaturePlot_DualAssay

Issue - State: closed - Opened by raunakkar 7 months ago - 3 comments
Labels: enhancement

#181 - DotPlot_scCustom: Show Cluster Idents on top

Issue - State: closed - Opened by jakob-arnold 7 months ago - 3 comments

#180 - Release v2.2.0

Pull Request - State: closed - Opened by samuel-marsh 7 months ago

#179 - as.anndata isseu

Issue - State: closed - Opened by lindsdudley 7 months ago - 5 comments

#178 - Access underlying matrix used in Clustered_DotPlot to remove NA/NaN/Inf

Issue - State: open - Opened by nehawali21 7 months ago - 13 comments
Labels: more-info-needed

#177 - Duplicate cell name error in Cell_Highlight_Plot, even though they are not duplicate

Issue - State: closed - Opened by yojetsharma 8 months ago - 9 comments
Labels: more-info-needed

#176 - Adding chicken to list of supported species?

Issue - State: closed - Opened by dpearton 8 months ago - 2 comments
Labels: enhancement

#175 - Merge_Seurat_List() add.cell.ids for long Seurat object list

Issue - State: closed - Opened by levinhein 8 months ago - 3 comments

#174 - Error in as.anndata object 'dim_reducs_list' not found

Issue - State: closed - Opened by moutazhelal 8 months ago - 1 comment

#173 - Use of DiscretePalette_scCustomize() with DimPlotPlus?

Issue - State: closed - Opened by charlotteharken 8 months ago - 16 comments

#172 - split.by error in Clustered_DotPlot function

Issue - State: closed - Opened by apal6 8 months ago - 6 comments
Labels: Not Working As Intended, more-info-needed

#171 - Allow to get unified legend when using split.by = "seurat_clusters" without having to use split_seurat = TRUE in DimPlot_scCustom()

Issue - State: closed - Opened by CroixJeremy2 8 months ago - 2 comments
Labels: bug

#170 - Clustered_DotPlot Plotting Meta Data when split.by

Issue - State: closed - Opened by samuel-marsh 8 months ago - 1 comment
Labels: bug

#169 - plot_median = TRUE does not work in VlnPlot_scCustom when features contains more than one gene

Issue - State: closed - Opened by CroixJeremy2 8 months ago - 1 comment

#168 - Help with getting as.anndata running

Issue - State: closed - Opened by jjia1 9 months ago - 17 comments
Labels: bug

#167 - Release Prep v2.2.0

Issue - State: closed - Opened by samuel-marsh 9 months ago - 3 comments
Labels: documentation, enhancement, New Feature, Vignette Related, Release Prep

#166 - Percent_Expressing doesn't work with chromatin assay

Issue - State: closed - Opened by cathynewman 9 months ago - 4 comments

#165 - Wrong R script "{overwrite = TRUE.} in Add_Cell_QC_Metrics

Issue - State: closed - Opened by chaesee1 9 months ago - 1 comment

#164 - plot_density_joint_only error

Issue - State: closed - Opened by yjjeong86 9 months ago - 1 comment

#162 - as.anndata issue

Issue - State: closed - Opened by williamsdrake 9 months ago - 2 comments
Labels: documentation, enhancement

#161 - Breaking changes in rliger

Issue - State: closed - Opened by theAeon 9 months ago - 57 comments
Labels: bug, enhancement, New Feature, Vignette Related, Release Prep

#160 - Adding SpatialPlots

Issue - State: closed - Opened by nina-hahn 9 months ago - 5 comments
Labels: enhancement, New Feature

#159 - aspect_ratio in 'Iterate_FeaturePlot_scCustom'

Issue - State: closed - Opened by palbioinfor 9 months ago - 7 comments
Labels: Not Working As Intended

#158 - group.by in DotPlot seems not working

Issue - State: closed - Opened by jasonleongbio 9 months ago - 6 comments
Labels: bug, Not Working As Intended

#157 - Release v2.1.0

Pull Request - State: closed - Opened by samuel-marsh 10 months ago

#156 - Feature Co-Expression

Issue - State: closed - Opened by pwmellors 10 months ago - 1 comment

#155 - Iterate FeaturePlot Multi

Issue - State: closed - Opened by samuel-marsh 11 months ago - 1 comment
Labels: bug, Not Working As Intended

#154 - Release Prep V2.1

Issue - State: closed - Opened by samuel-marsh 11 months ago - 2 comments
Labels: bug, documentation, enhancement, New Feature, Vignette Related, Release Prep

#153 - LIGER Function Fixes

Issue - State: closed - Opened by samuel-marsh 11 months ago
Labels: bug, enhancement

#152 - Clustered_DotPlot using active.ident for 3 groups

Issue - State: closed - Opened by EzequielD-86 11 months ago - 3 comments

#151 - Unable to re-install scCuztomise

Issue - State: closed - Opened by MeganS92 12 months ago - 3 comments

#150 - FeaturePlot_scCustom labels are incorrect when calling metadata and gene(feature) at the same time with split.by argument

Issue - State: closed - Opened by as-keller 12 months ago - 3 comments
Labels: bug, Not Working As Intended

GitHub / samuel-marsh/scCustomize issues and pull requests