Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / mojaveazure/seurat-disk issues and pull requests

#161 - Only a subset of scaled data available in .X

Issue - State: open - Opened by tessadgreen 11 months ago

#160 - Export all reductions in h5ad

Issue - State: open - Opened by bellenger-l 11 months ago

#156 - LoadH5Seurat no longer working for me

Issue - State: open - Opened by ccnawrocki 12 months ago

#154 - Error when saving Seurat to H5Seurat file with latest Seurat Version

Issue - State: open - Opened by ShanshanHe7 about 1 year ago - 1 comment

#153 - Error Loading Visium H5Seurat

Issue - State: open - Opened by BenjaminDEMAILLE about 1 year ago

#152 - Error when saving a Visium Seurat to H5Seurat

Issue - State: open - Opened by BenjaminDEMAILLE about 1 year ago - 1 comment

#150 - Matrix type mismatch when using LoadH5Seurat()

Issue - State: open - Opened by hlmtran about 1 year ago - 1 comment

#147 - Error in saveh5seurat after upgrading to Seurat v5

Issue - State: open - Opened by KristinAass about 1 year ago - 9 comments

#146 - Error in self$exists(name) : HDF5-API Errors:

Issue - State: open - Opened by imerelli over 1 year ago

#145 - Incompatability with latest version of anndata

Issue - State: open - Opened by LinearParadox over 1 year ago

#144 - Converting .rds (spatial transcriptomics) to anndata.

Issue - State: open - Opened by bogdan-bios over 1 year ago - 1 comment

#143 - Another issue with h5ad -> h5seurat

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

#141 - Problem with LoadH5Seurat

Issue - State: open - Opened by ydai3 over 1 year ago - 6 comments

#139 - Issues converting Anndata to h5seurat object

Issue - State: open - Opened by sarakn97 over 1 year ago

#138 - cell type annotation in metadata disappear

Issue - State: open - Opened by mimisikai over 1 year ago - 2 comments

#137 - Converting from .h5Seurat to h5ad messes up observational metadata

Issue - State: open - Opened by pakiessling over 1 year ago - 1 comment

#136 - Error in source[["var"]][[mf]]$read() : attempt to apply non-function

Issue - State: open - Opened by scauzhaos over 1 year ago - 5 comments

#135 - RStudio Crashes with LoadH5Seurat()

Issue - State: closed - Opened by sarakn97 over 1 year ago - 1 comment

#133 - Error when opening loom file generated by as.loom()

Issue - State: open - Opened by MartaBenegas over 1 year ago

#132 - Issues when subsetting and converting loom to seurat

Issue - State: open - Opened by HenriettaHolze over 1 year ago - 5 comments

#131 - Some questions about missing files in seuratdisk

Issue - State: open - Opened by HelloWorldLTY over 1 year ago

#130 - Suggestion: Append to h5Seurat file

Issue - State: open - Opened by Alkhawaja95 over 1 year ago

#128 - How could I convert a 'dgCmatrix' into '.h5' file?

Issue - State: open - Opened by jiangpuxuan almost 2 years ago

#127 - Conversion scrambles barcodes w/r/t metadata columns

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

#125 - Error: Missing required datasets 'levels' and 'values'

Issue - State: open - Opened by pmarzano97 almost 2 years ago - 3 comments

#122 - Error converting Tabula Sapiens h5ad files to h5seurat

Issue - State: open - Opened by taylordm almost 2 years ago - 9 comments

#121 - Error saving a Seurat object

Issue - State: open - Opened by msherafatian almost 2 years ago

#120 - Convert a scATAC data into h5Seurat

Issue - State: open - Opened by emanuelavilla almost 2 years ago

#119 - Source package available?

Issue - State: closed - Opened by michailk1982 about 2 years ago - 1 comment

#118 - Error in Loadh5Seurat

Issue - State: open - Opened by kguion1 about 2 years ago - 2 comments

#117 - `SparseWrite()` is now unavailable

Issue - State: open - Opened by shitiezhu about 2 years ago

#116 - Cannot re-install `seurat-disk`

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

#115 - Conversion from h5Seurat to h5ad not preserving gene names

Issue - State: open - Opened by shahrozeabbas about 2 years ago - 2 comments

#114 - SeuratDisk unavailable in R-Studio-Server

Issue - State: open - Opened by mar98trian about 2 years ago

#113 - Error reading h5seurat file

Issue - State: open - Opened by giorgiatosoni about 2 years ago

#112 - SaveH5Seurat output lacks UMAP slot

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

#111 - Error in Graphs(object = x) : could not find function "Graphs"

Issue - State: open - Opened by parkjooyoung99 about 2 years ago - 3 comments

#110 - Fix saving and loading of named vectors

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

#109 - Error: Missing required datasets 'levels' and 'values'

Issue - State: open - Opened by Diennguyen8290 about 2 years ago - 33 comments

#108 - Error in `Convert()` an `.h5Seurat` object into `.h5ad`.

Issue - State: open - Opened by jiangpuxuan over 2 years ago - 1 comment

#107 - anndata to seurat not working with scVI processed data

Issue - State: open - Opened by bjstewart1 over 2 years ago

#106 - Set encoding-type and encoding-version for 'var' in exported AnnData

Pull Request - State: closed - Opened by bbimber over 2 years ago - 2 comments

#105 - Exported AnnData lacks genes in the rownames (at least when read by python)

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

#104 - error saving updated Seurat (2.X -> 3.X) object

Issue - State: open - Opened by dtenenba over 2 years ago - 1 comment

#103 - Is this package usable?

Issue - State: open - Opened by pati-ni over 2 years ago

#102 - Missing meidum_umi in SCTModel obj - backward compatibility

Issue - State: open - Opened by simoncmo over 2 years ago - 5 comments

#101 - R object of all column names of a Loom file

Issue - State: open - Opened by alexandruioanvoda over 2 years ago

#100 - Error when convert H5ad to seurat object

Issue - State: open - Opened by GouQiao over 2 years ago - 6 comments

#99 - how to convert h5Seurat to h5ad for large object

Issue - State: open - Opened by FADHLyemen over 2 years ago

#98 - install on R version 3.6.0

Issue - State: open - Opened by DUAN-GAO over 2 years ago

#97 - Vector names dropped when loading from h5Seurat

Issue - State: closed - Opened by timoast over 2 years ago

#96 - Problem with Convert() from h5ad to h5seurat

Issue - State: open - Opened by Pazuzzilla over 2 years ago - 1 comment

#95 - problems with feature names in conversion of Seurat to AnnData

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

#94 - Error while using WriteH5Group() function

Issue - State: open - Opened by SaranjeetKaur over 2 years ago

#93 - Error: Cannot find feature names dataset at row_attrs/Gene

Issue - State: open - Opened by dm8000 over 2 years ago - 6 comments

#92 - Convert() fails on AnnData at metadata conversion step

Issue - State: open - Opened by dnjst almost 3 years ago - 1 comment

#91 - Have trouble saving H5Seurat files

Issue - State: open - Opened by sadiyarsh almost 3 years ago

#90 - Error in Convert

Issue - State: open - Opened by l-magnificence almost 3 years ago

#89 - Error in UseMethod DefaultAssay

Issue - State: open - Opened by nehad-procogia almost 3 years ago - 1 comment

#88 - C stack usage error during SaveH5Seurat call

Issue - State: closed - Opened by alexthiery almost 3 years ago - 1 comment

#87 - Convert all expression data

Issue - State: open - Opened by yjgeno almost 3 years ago

#82 - Error in converting h5ad to Seurat - Warning: Unknown file type: h5ad

Issue - State: open - Opened by fly4all about 3 years ago - 5 comments

#81 - Failure in SaveH5Seurat

Issue - State: open - Opened by GreenGilad about 3 years ago - 1 comment

#79 - How to convert from Seurat visium to AnnData

Issue - State: open - Opened by hzongyao about 3 years ago - 3 comments

#77 - LoadH5Seurat error: Too many values for levels provided

Issue - State: open - Opened by carcinas about 3 years ago - 7 comments

#76 - Issue loading h5ad/h5seurat

Issue - State: open - Opened by li-xuyang28 about 3 years ago - 1 comment

#75 - Conversion of h5Seurat object to h5ad not capturing RNA assay after integration

Issue - State: open - Opened by hsmaan about 3 years ago - 6 comments

#73 - Fixed filename bug h5Seurat vs of h5seurat

Pull Request - State: closed - Opened by GreenGilad about 3 years ago - 1 comment

#71 - Issue with saving h5ad file after Convert

Issue - State: closed - Opened by FloWuenne about 3 years ago - 1 comment

#69 - only 2K genes found after converting seurat object to AnnData

Issue - State: open - Opened by gt7901b about 3 years ago - 2 comments

#67 - spatial RDS lost image information after being convered to h5ad

Issue - State: open - Opened by yingfang3333 about 3 years ago - 6 comments

#62 - Need to support sparse matrix transform from anndata to Seraut object

Issue - State: open - Opened by songtingstone over 3 years ago - 1 comment

#55 - Installation error SeuratDisk

Issue - State: closed - Opened by SaraVerbandt over 3 years ago - 1 comment

#54 - SaveH5Seurat failing on example mouse bone marrow dataset

Issue - State: open - Opened by GBeattie over 3 years ago - 3 comments

#52 - Error in Graphs(object = x) : could not find function "Graphs"

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

#51 - Strange h5.ad conversion error

Issue - State: closed - Opened by akhst7 over 3 years ago

#50 - Error loading .h5ad file to Scvelo

Issue - State: closed - Opened by akhst7 over 3 years ago - 2 comments

#33 - Error converting h5ad file

Issue - State: open - Opened by Vivianstats over 3 years ago - 1 comment

#32 - h5ad->Seurat:Not a sparse matrix

Issue - State: open - Opened by AlexStewart25 over 3 years ago - 2 comments

#30 - Convert Error in dfile$obj_copy_from

Issue - State: open - Opened by igordot over 3 years ago - 41 comments

#29 - Error in Initializing RNA with data

Issue - State: open - Opened by paupuigdevall over 3 years ago - 4 comments

#27 - Error when saving h5seurat

Issue - State: closed - Opened by ccruizm over 3 years ago - 7 comments