Package: SeuratDisk 0.0.0.9021

Paul Hoffman

SeuratDisk: Interfaces for HDF5-Based Single Cell File Formats

The h5Seurat file format is specifically designed for the storage and analysis of multi-modal single-cell and spatially-resolved expression experiments, for example, from CITE-seq or 10X Visium technologies. It holds all molecular information and associated metadata, including (for example) nearest-neighbor graphs, dimensional reduction information, spatial coordinates and image data, and cluster labels. We also support rapid and on-disk conversion between h5Seurat and AnnData objects, with the goal of enhancing interoperability between Seurat and Scanpy.

Authors:Paul Hoffman [aut, cre], Rahul Satija [ctb]

SeuratDisk_0.0.0.9021.tar.gz
SeuratDisk_0.0.0.9021.zip(r-4.7)SeuratDisk_0.0.0.9021.zip(r-4.6)SeuratDisk_0.0.0.9021.zip(r-4.5)
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SeuratDisk_0.0.0.9021.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SeuratDisk/json (API)

# Install 'SeuratDisk' in R:
install.packages('SeuratDisk', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mojaveazure/seurat-disk/issues

Pkgdown/docs site:https://mojaveazure.github.io

On CRAN:

Conda:

hdf5-formatsingle-cell-genomicssingle-cell-rna-seq

7.78 score 175 stars 1 packages 5.7k scripts 20 exports 146 dependencies

Last updated from:877d4e18ab. Checks:7 WARNING, 1 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING253
source / vignettesERROR485
linux-release-x86_64WARNING260
macos-release-arm64WARNING130
macos-oldrel-arm64WARNING140
windows-develWARNING201
windows-releaseWARNING183
windows-oldrelWARNING188
wasm-releaseOK164

Exports:AppendDataas.factoras.h5Seuratas.listas.loomConnectConvertGetSCDiskh5SeuratLoadH5SeuratLoadLoomloomreadH5AD_obsreadH5AD_obsmRegisterSCDiskSaveH5SeuratSaveLoomscdiskTransposeWriteH5Group

Dependencies:abindaskpassbase64encBHbitbit64bitopsbslibcachemcaToolscliclustercodetoolscommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolshdf5rherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemimeminiUInlmeopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS7sassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo

Readme and manuals

Help Manual

Help pageTopics
SeuratDisk: Interfaces for HDF5-Based Single Cell File FormatsSeuratDisk-package SeuratDisk _PACKAGE
Append data from an h5Seurat file to a preexisting 'Seurat' objectAppendData AppendData.character AppendData.H5File AppendData.h5Seurat
Connect to a single-cell HDF5 datasetConnect
Convert an on-disk single-cell dataset to another formatConvert Convert.character Convert.H5File Convert.h5Seurat
Seurat bindings for h5Seurat filesCells Cells.h5Seurat DefaultAssay DefaultAssay.h5Seurat DefaultAssay<-.h5Seurat h5Seurat-bindings Idents Idents.h5Seurat IsGlobal IsGlobal.H5Group Key Key.H5Group Project Project.h5Seurat Project<-.h5Seurat Stdev.h5Seurat
A class for connections to h5Seurat filesh5Seurat h5Seurat-class
Load a saved 'Seurat' object from an h5Seurat fileas.Seurat as.Seurat.h5Seurat LoadH5Seurat LoadH5Seurat.character LoadH5Seurat.H5File LoadH5Seurat.h5Seurat
Loom-file Loadingas.Seurat as.Seurat.loom LoadLoom LoadLoom.character LoadLoom.H5File LoadLoom.loom
Seurat binding for loom filesDefaultAssay DefaultAssay.loom dim dim.loom loom-bindings
A class for connections to loom filesloom loom-class
Load data from an HDF5 Fileas.array as.array.H5D as.data.frame as.data.frame.H5D as.data.frame.H5Group as.factor as.factor,H5Group-method as.list as.list,H5Group-method as.logical as.logical.H5D as.matrix as.matrix.H5D as.matrix.H5Group as.sparse as.sparse.H5D as.sparse.H5Group dimnames dimnames.H5D ReadH5
Get and Register 'scdisk' SubclassesGetSCDisk RegisterSCDisk
Save a 'Seurat' object to an h5Seurat fileas.h5Seurat as.h5Seurat.default as.h5Seurat.H5File as.h5Seurat.Seurat SaveH5Seurat SaveH5Seurat.default SaveH5Seurat.Seurat
Save a 'Seurat' object to a loom fileas.loom as.loom.default as.loom.H5File as.loom.Seurat SaveLoom SaveLoom.default SaveLoom.Seurat
A disk-based object for single-cell analysisscdisk scdisk-class
Transpose a matrixTranspose Transpose.dgCMatrix Transpose.H5D Transpose.H5Group
Write data to an HDF5 groupWriteH5Group WriteH5Group,ANY-method WriteH5Group,array-method WriteH5Group,Assay-method WriteH5Group,data.frame-method WriteH5Group,dgCMatrix-method WriteH5Group,DimReduc-method WriteH5Group,factor-method WriteH5Group,Graph-method WriteH5Group,list-method WriteH5Group,logical-method WriteH5Group,Neighbor-method WriteH5Group,SeuratCommand-method