samuel-marsh/scCustomize

Issues

• About the scCustomize package dependent package error

  #215 opened 2 months ago by PanSX-Dr
  4

• scCustomize generating empty plots

  #213 opened 2 months ago by rasing02
  10

• release/3.0.0 install issue

  #214 opened 2 months ago by aherman-umn
  1

• as.anndata raises error in which(): argument to which () is not logical

  #207 opened 3 months ago by tjm-sci
  3

• Iterate_FeaturePlot_scCustom error

  #210 opened 2 months ago by mph270
  3

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

  #208 opened 2 months ago by mph270
  7

• conversion to anndata

  #188 opened 5 months ago by Flu09
  17

• Option to change dot size in Clustered_DotPlot()?

  #211 opened 2 months ago by reyancoskun
  1

• Bug fixes (Plot_Density_Custom and Plot_Density_Joint_Only drawing) ；Picture saving

  #212 opened 2 months ago by Roner2022
  1

• Updated_HGNC_Symbols tries to download from non-existent site.

  #209 opened 2 months ago by Abiologist
  1

• as.anndata isseu

  #179 opened 8 months ago by lindsdudley
  5

• split.by error in Clustered_DotPlot function

  #172 opened 8 months ago by apal6
  6

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

  #191 opened 5 months ago by denvercal1234GitHub
  2

• as.anndata error with which(single_val_columns)) argument to 'which' is not logical

  #206 opened 3 months ago by brainfo
  3

• "split.by" option in Cluster Highlight Plot caused error

  #201 opened 4 months ago by jasonleongbio
  3

• When converting from Seurat RDS to anndata h5ad, gene names are lost.

  #195 opened 3 months ago by joshuak94
  9

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

  #205 opened 3 months ago by Runzhi819
  1

• Release 3.0.0

  #204 opened 4 months ago by samuel-marsh
  0

• Release Prep v2.2.0

  #167 opened 4 months ago by samuel-marsh
  3

• DotPlot_scCustom: Show Cluster Idents on top

  #181 opened 4 months ago by jakob-arnold
  3

• Updated_HGNC_Symbols using mouse genes

  #202 opened 4 months ago by siv2108
  2

• request pass parameters to ComplexHeatmap::Heatmap

  #199 opened 4 months ago by johnminglu
  9

• 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

  #200 opened 4 months ago by CroixJeremy2
  2

• Error Merge

  #187 opened 4 months ago by eblchen
  11

• unused argument (alpha = alpha_exp) erro in FeaturePlot_scCustom

  #197 opened 4 months ago by shanshancode
  4

• Clarification regarding `exp_value_type = "scaled"` in `scCustomize::Clustered_DotPlot`

  #196 opened 4 months ago by denvercal1234GitHub
  1

• Adjusting font size with theme() does not work with figure_plot = TRUE

  #194 opened 5 months ago by wendelljpereira
  1

• "reduction" argument missing on "Cluster Highlight Plot" man page

  #198 opened 4 months ago by jasonleongbio
  1

• Setting a scale/limit for `scCustomize::Plot_Density_Custom`?

  #192 opened 5 months ago by denvercal1234GitHub
  6

• ! Column name `barcodes` must not be duplicated.

  #193 opened 5 months ago by Flu09
  2

• Due to error in Nebulosa package and ggplot2 v3.5.0

  #190 opened 5 months ago by XIANZHE-LI
  2

• Help with getting as.anndata running

  #168 opened 10 months ago by jjia1
  17

• Enable `Add_Cell_QC_Metrics()` to Support ENSEMBL IDs for "IEG" and "MSig_DB"

  #186 opened 7 months ago by JuanTejedor
  2

• Plots not printing

  #185 opened 8 months ago by hcjarnagin
  2

• Duplicate cell name error in Cell_Highlight_Plot, even though they are not duplicate

  #177 opened 8 months ago by yojetsharma
  9

• Set different color palettes to be used for different assays in FeaturePlot_DualAssay

  #182 opened 8 months ago by raunakkar
  3

• Add_Mito_Ribo multiple species

  #184 opened 8 months ago by rhart604
  3

• MAD_stats mad_num variable doesn't change value

  #183 opened 8 months ago by chloetu-dfci
  5

• Access underlying matrix used in Clustered_DotPlot to remove NA/NaN/Inf

  #178 opened 8 months ago by nehawali21
  13

• Adding chicken to list of supported species?

  #176 opened 9 months ago by dpearton
  2

• Merge_Seurat_List() add.cell.ids for long Seurat object list

  #175 opened 9 months ago by levinhein
  3

• Error in as.anndata object 'dim_reducs_list' not found

  #174 opened 9 months ago by moutazhelal
  1

• Use of DiscretePalette_scCustomize() with DimPlotPlus?

  #173 opened 9 months ago by charlotteharken
  16

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

  #171 opened 9 months ago by CroixJeremy2
  2

• Clustered_DotPlot Plotting Meta Data when split.by

  #170 opened 9 months ago by samuel-marsh
  1

• plot_median = TRUE does not work in VlnPlot_scCustom when features contains more than one gene

  #169 opened 9 months ago by CroixJeremy2
  1

• as.anndata issue

  #162 opened 10 months ago by williamsdrake
  2

• Percent_Expressing doesn't work with chromatin assay

  #166 opened 10 months ago by cathynewman
  4

• Wrong R script "{overwrite = TRUE.} in Add_Cell_QC_Metrics

  #165 opened 10 months ago by chaesee1
  1

• plot_density_joint_only error

  #164 opened 10 months ago by yjjeong86
  1