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from rlang (#178)UpdateSeuratObject
(@ddiez, #182)...
to call signature for Radius
generic (#190)PolyVtx
(#194)UpdateSeuratObject
to run without Seurat
installed (#199)Layers.Assay()
when the search returns no results (@maxim-h, #189)subset
to allow empty images to be dropped (#204)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.
Health stats visible at Monitor.