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
#159 - Error: "Failed to install 'unknown package' from GitHub: Timeout was reached" while installing SeuratDisk, R version 4.1.1, Platform: x86_64-w64-mingw32/x64 (64-bit)
Issue -
State: open - Opened by aanu28 11 months ago
#158 - error in curl::curl_download() step:Failed to open file pbmc3k_final.h5ad.curltmp.
Issue -
State: open - Opened by Sophia409 11 months ago
#157 - Error in converting h5ad to h5Seurat Error: (converted from warning) Unknown file type: h5ad
Issue -
State: open - Opened by Sophia409 11 months ago
#156 - LoadH5Seurat no longer working for me
Issue -
State: open - Opened by ccnawrocki 12 months ago
#155 - How do i download a older version of SeuratDisk
Issue -
State: open - Opened by tushar-dhyani-elucidata about 1 year 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
#151 - Error: Attempting to add a different number of cells and/or features
Issue -
State: open - Opened by sarahbonnin about 1 year ago
#150 - Matrix type mismatch when using LoadH5Seurat()
Issue -
State: open - Opened by hlmtran about 1 year ago
- 1 comment
#149 - HDF5-API Errors: error #000: H5Ocopy.c in H5Ocopy(): line 240: unable to copy object
Issue -
State: open - Opened by catsargent about 1 year ago
#148 - error Convert("test.h5seurat", dest = "h5ad", overwrite = TRUE)
Issue -
State: open - Opened by wang0430 about 1 year ago
#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$exists(name) : HDF5-API Errors:
Issue -
State: open - Opened by imerelli over 1 year ago
#145 - Incompatability with latest version of anndata
Issue -
State: open - Opened by LinearParadox over 1 year ago
#144 - Converting .rds (spatial transcriptomics) to anndata.
Issue -
State: open - Opened by bogdan-bios over 1 year ago
- 1 comment
#143 - Another issue with h5ad -> h5seurat
Issue -
State: closed - Opened by bennjmo over 1 year ago
- 1 comment
#142 - AnnData to h5seurat not working via rpy2/jupyter notebook
Issue -
State: open - Opened by jesswhitts over 1 year ago
#141 - Problem with LoadH5Seurat
Issue -
State: open - Opened by ydai3 over 1 year ago
- 6 comments
#140 - Merging two .h5seurat files containing ATAC assays renders them unsaveable using SaveH5Seurat
Issue -
State: open - Opened by volkansevim over 1 year ago
#139 - Issues converting Anndata to h5seurat object
Issue -
State: open - Opened by sarakn97 over 1 year ago
#138 - cell type annotation in metadata disappear
Issue -
State: open - Opened by mimisikai over 1 year ago
- 2 comments
#137 - Converting from .h5Seurat to h5ad messes up observational metadata
Issue -
State: open - Opened by pakiessling over 1 year ago
- 1 comment
#136 - Error in source[["var"]][[mf]]$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
#134 - Error in if (!all(cur_arg > 0)) { : missing value where TRUE/FALSE needed
Issue -
State: open - Opened by denvercal1234GitHub over 1 year ago
- 6 comments
#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
#129 - Trying to convert h5ad file to h5seurat and producing file in directory but cannot open
Issue -
State: open - Opened by mwu2001 almost 2 years ago
- 2 comments
#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
#126 - Convert H5Seurat to AnnDisk failure when metadata col has all NA
Issue -
State: open - Opened by bbimber almost 2 years ago
#125 - Error: Missing required datasets 'levels' and 'values'
Issue -
State: open - Opened by pmarzano97 almost 2 years ago
- 3 comments
#124 - I tried to convert from a HD5ad file to h5seurat using convert function in seurat-disk package, but it failed with this error message "Error: Cannot find feature names in this H5AD file"
Issue -
State: open - Opened by peralesvilchezl almost 2 years ago
- 1 comment
#123 - How to set adata.var.index as gene name but not index number by SeuratDisk
Issue -
State: open - Opened by UboCA almost 2 years ago
#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
#86 - Error: 'Images' is not an exported object from 'namespace:Seurat'
Issue -
State: open - Opened by gt7901b 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
#63 - When installing seurat-disk, there is a bug, which says "ERROR: lazy loading failed for package 'SeuratDisk' * removing 'C:/Users/user/Documents/R/win-library/4.0/SeuratDisk'"
Issue -
State: open - Opened by zhangleiju about 3 years ago
- 10 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
#61 - Interoperability with scvelo, SeuratDisk::as.loom fails to store umap embeddings in loom object
Issue -
State: open - Opened by tslimax 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
#37 - Support the custom gene/cell data query directly on the sparse matrix.
Pull Request -
State: closed - Opened by zhanghao-njmu over 3 years ago
#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