Cannot find feature names in this h5ad file
WebApr 12, 2024 · Thanks for contributing an answer to Stack Overflow! Please be sure to answer the question.Provide details and share your research! But avoid …. Asking for … WebMay 21, 2024 · Convert( source=scanpy_src, dest="h5Seurat", overwrite=TRUE, verbose=TRUE ) This created the following messages: Warning message: “Unknown file type: h5ad” Warning message: “'assay' not set, setting to 'RNA'” Creating h5Seurat file for version 3.1.2 Adding X as data Adding raw/X as counts Adding meta.features from …
Cannot find feature names in this h5ad file
Did you know?
WebFixFeatures: Fix Feature Names; GetClass: Get a class string with package information; GetMargin: Determine the margin to use for a dataset; GetObject: Figure out which objects to load from an h5Seurat file; ... ("Cannot find scaled features in … WebJun 3, 2024 · Issue loading h5ad/h5seurat · Issue #76 · mojaveazure/seurat-disk · GitHub mojaveazure / seurat-disk Public Notifications Fork 39 Star 93 Code Issues 104 Pull requests 1 Security Insights New issue Issue loading h5ad/h5seurat #76 Open li-xuyang28 opened this issue on Jun 3, 2024 · 1 comment li-xuyang28 commented on Jun 3, 2024 …
WebJul 10, 2024 · what is the .h5ad file? · Issue #180 · scverse/anndata · GitHub scverse / anndata Public Notifications Fork 124 Star 360 Code Issues 214 Pull requests 50 Actions Projects 1 Security Insights New issue what is the .h5ad file? #180 Closed fenghuijian opened this issue on Jul 10, 2024 · 3 comments fenghuijian on Jul 10, 2024 WebFeb 11, 2024 · When I loaded the h5ad file, the feature names were always missing (numbers only): a = ReadH5AD('XXX.h5ad') Pulling expression matrices and metadata …
WebApr 5, 2024 · Validating h5Seurat file Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-') Initializing RNA with data Adding counts for RNA Adding feature-level metadata for RNA Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-') Initializing combat_corrected with data Adding counts for … WebSaving a dataset. Saving a Seurat object to an h5Seurat file is a fairly painless process. All assays, dimensional reductions, spatial images, and nearest-neighbor graphs are automatically saved as well as extra metadata such as miscellaneous data, command logs, or cell identity classes from a Seurat object. To save a Seurat object, we need the Seurat …
WebWhen reading: project name is basename (file); identity classes will be set as the project name; all cell-level metadata from adata.obs will be taken; feature level metadata from data.var and adata.raw.var (if present) will be merged and stored in assay meta.features; highly variable features will be set if highly_variable is present in …
WebApr 30, 2024 · Convert h5Seurat files to H5AD files Description Convert h5Seurat files to H5AD files Usage H5SeuratToH5AD ( source, dest, assay = DefaultAssay (object = source), overwrite = FALSE, verbose = TRUE ) Arguments Value Returns a handle to dest as an H5File object h5Seurat to AnnData/H5AD the graw havre de grace mdWebSaving a dataset. Saving a Seurat object to an h5Seurat file is a fairly painless process. All assays, dimensional reductions, spatial images, and nearest-neighbor graphs are … theatrhythm final bar line testWebMar 5, 2024 · Error: Cannot acccess information in H5AD file · Issue #53 · mojaveazure/seurat-disk · GitHub mojaveazure / seurat-disk Public Notifications Fork 38 Star 90 Code Issues Pull requests Security Insights Error: Cannot acccess information in H5AD file #53 Open errcricket opened this issue on Mar 5, 2024 · 0 comments commented theatrhythm final bar line teamsWeb.uns['mast_diff_res_columns']: Column names for the differential expression ... (url_Rep3, basename(url_Rep3)) #H5AD files are compressed using the LZF filter. #This filter is Python-specific, and cannot easily be used in R. ... (url_Rep3, basename(url_Rep3)) #H5AD files are compressed using the LZF filter. #This filter is Python-specific, and ... the grawlix podcasttheatrhythm final bar line switch cheatsWebApr 1, 2024 · Trying to convert h5ad file to h5seurat and producing file in directory but cannot open HOT 2 Suggestion: Append to h5Seurat file Some questions about missing files in seuratdisk theatrhythm final bar line versionsWebDec 7, 2024 · UpdateSymbolList function to pull new gene names from HGNC; Added support for H5AD layers as additional assays in a Seurat object; Changed. Fix rownames issue when running UMAP on dist object; Add support for new H5AD obsm and varm stucture; Fix issue when trying to read non-existent feature-level metadata from an … thegray16