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GetAssayData()
to use layer
instead of slot
(#160)SaveSeuratRds()
to move all layers instead of just those in tempdir()
(#169)SetAssayData()
to use layer
instead of slot
(#171)FilterObjects()
to .FilterObjects()
(#171)Assay5
class with support for layers; layers provide support for:
$
method for Assay
and Assay5
objects to pull expression matrices, replacing informal usage of @
LayerData()
and LayerData()<-
functions to replace GetAssayData()
and SetAssayData()
, respectivelydimnames()<-
(changing feature names does not apply to v3 Assay
objects)SaveSeuratRds()
and LoadSeuratRds()
to save and load Seurat
objects with disk-backed layersdroplevels.LogMap()
to drop unused entries from a LogMap
split()
) and rejoin layers (JoinLayers()
) within Assay
and Assay5
objects based on grouping factorslot
argument deprecated in all contexts; where applicable, replaced with layer
argument[
for Assay
and Assay5
objects take a layer name to pull an expression matrix
Seurat.object.assay.brackets
allows restoring v3/v4 behavior of subsetting the main expression matrix (eg. data
)PackageCheck()
deprecated in favor of rlang::check_installed()
AttachDeps()
deprecated in favor of using the Depends
field of DESCRIPTION
Seurat
object may have subsets of cells present at the object levelstop()
and warning()
with rlang::abort()
and rlang::warn()
for easier debuggingKeyMixin
objectsAssay()
, Seurat()
)CellsByIdentities
(#80)Assays
and DimReducs
in UpdateSeuratObject
when missingUpdateSeuratObject
to work when data
is NULL
(#38)FOV
, Segmentations
, Centroids
, and Molecules
classes for imaging-based spatial datasetsCreateSeuratObject.Assay
sets Assay key when not present (#29)Assay
from a data frame (#32)CheckMatrix
generic for validating expression matricesKey.Seurat
(#26)Seurat.checkdots
option if option is not set (#16)head
and tail
methods for Seurat
and Assay
objects (#5)AttachDeps
to attach required imported dependencies on package attachmentIsMatrixEmpty
to test if a matrix is empty or notAssay
objects to replace Seurat::SCTAssay
or Signac::ChromatinAssay
objects of the same namedata.table
/tibble
objects (#4)NULL
if a subset results in zero cells (#9)These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.