Ecosyste.ms: Issues

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GitHub / samuel-marsh/scCustomize issues and pull requests

#204 - Release 3.0.0

Issue - State: open - Opened by samuel-marsh 19 days ago
Labels: documentation, enhancement, New Feature, Vignette Related, Release Prep

#203 - Release/3.0.0

Pull Request - State: open - Opened by samuel-marsh 19 days ago

#202 - Updated_HGNC_Symbols using mouse genes

Issue - State: closed - Opened by siv2108 26 days ago - 2 comments
Labels: enhancement, New Feature

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

Issue - State: closed - Opened by jasonleongbio 29 days ago - 1 comment

#199 - request pass parameters to ComplexHeatmap::Heatmap

Issue - State: closed - Opened by johnminglu about 1 month ago - 9 comments
Labels: enhancement, more-info-needed

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

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

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

Issue - State: closed - Opened by shanshancode about 2 months ago - 4 comments
Labels: bug, more-info-needed

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

Issue - State: open - Opened by joshuak94 about 2 months ago - 8 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 about 2 months ago - 1 comment

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

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

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

Issue - State: closed - Opened by denvercal1234GitHub about 2 months ago - 6 comments

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

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

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

Pull Request - State: closed - Opened by fbearoff 2 months ago - 1 comment

#188 - conversion to anndata

Issue - State: closed - Opened by Flu09 4 months ago - 15 comments
Labels: more-info-needed

#187 - Error Merge

Issue - State: closed - Opened by eblchen 4 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 5 months ago - 2 comments
Labels: enhancement

#185 - Plots not printing

Issue - State: closed - Opened by hcjarnagin 5 months ago - 2 comments
Labels: more-info-needed

#184 - Add_Mito_Ribo multiple species

Issue - State: closed - Opened by rhart604 5 months ago - 3 comments
Labels: enhancement

#183 - MAD_stats mad_num variable doesn't change value

Issue - State: closed - Opened by chloetu-dfci 5 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 5 months ago - 3 comments
Labels: enhancement

#181 - DotPlot_scCustom: Show Cluster Idents on top

Issue - State: closed - Opened by jakob-arnold 5 months ago - 3 comments

#180 - Release v2.2.0

Pull Request - State: closed - Opened by samuel-marsh 6 months ago

#179 - as.anndata isseu

Issue - State: closed - Opened by lindsdudley 6 months ago - 3 comments

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

Issue - State: open - Opened by nehawali21 6 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 6 months ago - 9 comments
Labels: more-info-needed

#176 - Adding chicken to list of supported species?

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

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

Issue - State: closed - Opened by levinhein 6 months ago - 3 comments

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

Issue - State: closed - Opened by moutazhelal 6 months ago - 1 comment

#173 - Use of DiscretePalette_scCustomize() with DimPlotPlus?

Issue - State: closed - Opened by charlotteharken 6 months ago - 16 comments

#172 - split.by error in Clustered_DotPlot function

Issue - State: closed - Opened by apal6 6 months ago - 5 comments
Labels: Not Working As Intended, more-info-needed

#170 - Clustered_DotPlot Plotting Meta Data when split.by

Issue - State: closed - Opened by samuel-marsh 7 months ago - 1 comment
Labels: bug

#168 - Help with getting as.anndata running

Issue - State: closed - Opened by jjia1 7 months ago - 17 comments
Labels: bug

#167 - Release Prep v2.2.0

Issue - State: closed - Opened by samuel-marsh 7 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 7 months ago - 4 comments

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

Issue - State: closed - Opened by chaesee1 7 months ago - 1 comment

#164 - plot_density_joint_only error

Issue - State: closed - Opened by yjjeong86 7 months ago - 1 comment

#162 - as.anndata issue

Issue - State: closed - Opened by williamsdrake 7 months ago - 2 comments
Labels: documentation, enhancement

#161 - Breaking changes in rliger

Issue - State: closed - Opened by theAeon 7 months ago - 57 comments
Labels: bug, enhancement, New Feature, Vignette Related, Release Prep

#160 - Adding SpatialPlots

Issue - State: closed - Opened by nina-hahn 7 months ago - 5 comments
Labels: enhancement, New Feature

#159 - aspect_ratio in 'Iterate_FeaturePlot_scCustom'

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

#158 - group.by in DotPlot seems not working

Issue - State: closed - Opened by jasonleongbio 8 months ago - 6 comments
Labels: bug, Not Working As Intended

#157 - Release v2.1.0

Pull Request - State: closed - Opened by samuel-marsh 8 months ago

#156 - Feature Co-Expression

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

#155 - Iterate FeaturePlot Multi

Issue - State: closed - Opened by samuel-marsh 9 months ago - 1 comment
Labels: bug, Not Working As Intended

#154 - Release Prep V2.1

Issue - State: closed - Opened by samuel-marsh 9 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 9 months ago
Labels: bug, enhancement

#152 - Clustered_DotPlot using active.ident for 3 groups

Issue - State: closed - Opened by EzequielD-86 10 months ago - 3 comments

#151 - Unable to re-install scCuztomise

Issue - State: closed - Opened by MeganS92 10 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 10 months ago - 3 comments
Labels: bug, Not Working As Intended

#149 - Using Clustered_DotPlot function

Issue - State: closed - Opened by isaiao01 10 months ago - 5 comments
Labels: Not Working As Intended, more-info-needed

#148 - Add option to control stroke size for plotting smaller dots

Issue - State: closed - Opened by nikofleischer 10 months ago - 3 comments

#147 - Request option to change colour of NA values when plotting

Issue - State: closed - Opened by SamuelCWJ 10 months ago - 3 comments
Labels: more-info-needed

#145 - setting combine = FALSE in Plot_Density_Custom() returns NULL

Issue - State: closed - Opened by Brawni 10 months ago - 2 comments
Labels: more-info-needed

#144 - "alpha_exp" changing the transparency of the scalebar and not the points.

Issue - State: closed - Opened by ishwarvh 10 months ago - 3 comments

#143 - Split_FeatureScatter

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

#142 - Release/2.0.1

Pull Request - State: closed - Opened by samuel-marsh 11 months ago

#141 - Release/2.0.0

Pull Request - State: closed - Opened by samuel-marsh 11 months ago

#139 - Clustered_Doptplot by feature groups

Issue - State: closed - Opened by marshelma 11 months ago - 2 comments

#138 - Release/2.0.0

Pull Request - State: closed - Opened by samuel-marsh 11 months ago

#137 - Error in DelayedArray::colAutoGrid(x = counts, ncol = length(x = layer.cells))

Issue - State: closed - Opened by kenneditodd 11 months ago - 4 comments
Labels: bug, more-info-needed

#136 - Do sccustomize has an RRID entry?

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

#135 - Featureplot color scale limits

Issue - State: closed - Opened by Prathyusha-konda 12 months ago - 4 comments

#134 - Split.plot feature for stacked violin plots.

Issue - State: closed - Opened by Chanukya-Pavan 12 months ago - 1 comment

#133 - Error in `Add_Mito_Ribo_Seurat

Issue - State: closed - Opened by amv33576 12 months ago - 3 comments
Labels: bug, more-info-needed

#132 - error in Cluster_Highlight_Plot when raster = T

Issue - State: closed - Opened by Eomesodermin 12 months ago - 6 comments
Labels: bug

#131 - Prepare for upcoming Seurat v5 Release

Issue - State: closed - Opened by Gesmira almost 1 year ago - 3 comments
Labels: Release Prep

#130 - Calculate_joint_density

Issue - State: closed - Opened by PrashINRA about 1 year ago - 3 comments

#129 - Request dot scale parameter for Clustered_DotPlot

Issue - State: closed - Opened by Evenlyeven about 1 year ago - 4 comments
Labels: enhancement

#127 - offer figure_plot = TRUE for FeaturePlot_scCustom

Issue - State: closed - Opened by wwzhang about 1 year ago - 6 comments
Labels: enhancement

#126 - Move from base to fs for read functions and Iterative Plotting

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

#125 - Merge develop into V5dev

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

#124 - Problem with reading multiple h5 files using Read10X_h5_Multi_Directory()

Issue - State: closed - Opened by peculiar97 about 1 year ago - 7 comments

#123 - Fix Feature_PreCheck in Iterative Plots & Param Names

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

#122 - Hidden messages showing

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

#121 - QC Plot UMI vs Gene Remove 1 Legend

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

#120 - DimPlot_scCustom error ordering

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

#119 - Test parallel processing pbapply frameworks

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

#118 - Create Dual Assay Seurat Object error

Issue - State: closed - Opened by dgrutherford about 1 year ago - 11 comments
Labels: bug

#117 - Cluster_Stats_All_Samples no longer working

Issue - State: closed - Opened by emily-003 about 1 year ago - 3 comments

#116 - Split_FeatureScatter missing correlation output

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

#115 - Read_Metrics_10X error

Issue - State: closed - Opened by rhart604 about 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 about 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 about 1 year ago - 2 comments

#112 - Release/1.1.2

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

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

Issue - State: closed - Opened by samuel-marsh about 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

#104 - Merge_Sparse_Data_All with multimodal sparse matrices

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