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subset.Seurat to no longer call
droplevels on the input’s cell-level meta.data
slot; update subset.Assay to no longer call
droplevels on the input’s feature-level
meta.features slot; update subset.StdAssay to
no longer call droplevels on the input’s feature-level
meta.data slot (reverting #251, see discussion in
#247)drop = FALSE when retrieving data in
LayerData.Assay to preserve dimensions when subsetting to
the requested cells (#261)sf.data slot in the Segmentation
class to store a data.frame in accordance with changes in
loading Visium segmentations (#267)compact slot to the Segmentation class
to denote whether the object only stores segmentation information in the
sf.data slot, or also the sp-inherited slots
(#267)CreateSegmentation,
CreateSegmentation.data.frame,
CreateSegmentation.sf, and methods interacting with
Segmentation objects (Cells.Segmentation,
RenameCells.Segmentation, Crop.Segmentation,
subset.Segmentation, [[<-,
coordinates, Overlay, show,
setValidity) to account for the addition of
compact and the update to sf.data
coords_x_orientation slot to the FOV
class to hold the orientation of the x-axis for spatial data (to mark
whether the coordinate system of a spatial object has been updated)UpdateSeuratObject to check whether an object
requires an update to the coordinate system based on the existence and
value of the coords_x_orientation slot (currently only
relevant for Visium objects)safeValidityCheck to show an improved error
message suggesting to run UpdateSeuratObject when a “slots
in class definition but not in object” error is thrown by R’s internal
object validation; use in FOV-interacting methodssf.data slot to the Segmentation class
to store an sf
object (#258)
sf.data will represent segmentation boundaries for a
given image inside the images slot of a Seurat objectCreateSegmentation.sf, [[<-,
setValidity for interacting with Segmentation
objectsRenameCells.Segmentation,
subset.Segmentation, [,
UpdateSeuratObjectmisc slot to SpatialImage to
store additional info associated with an object in a list (#258)subset.Seurat to call droplevels on
the input’s cell-level meta.data slot; update
subset.Assay to call droplevels on the input’s
feature-level meta.features slot; update
subset.StdAssay to call droplevels on the
input’s feature-level meta.data slot (#251)UpdateSeuratObject to call
droplevels on the input’s cell-level meta.data
slot (@samuel-marsh, #247)Seurat from Enhances; update
.IsFutureSeurat to avoid calling
requireNamespace('Seurat', ...) (#250)VariableFeatures.StdAssay setter to apply a
speedup (#240)SVFInfo.Assay5 &
SpatiallyVariableFeatures.Assay5 (#242)UpdateSeuratObject (@neanderthalensis, #210)WhichCells.Seurat (@maxim-h, #219)SpatiallyVariableFeatures.Assay (#242)merge.Seurat (#246)VariableFeatures.StdAssay (#245)HVFInfo.StdAssay (#244)RenameCells.Seurat (#237)subset.StdAssay (#214)%||% 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
LogMapsplit()) 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 DESCRIPTIONSeurat 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.