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AustinHartmanAustinHartman
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Merge pull request #6758 from satijalab/release/4.3.0
Seurat v4.3.0
2 parents 0905a17 + ff03fdf commit 763259d

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‎DESCRIPTION

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Package: Seurat
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Version: 4.2.1
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Date: 2022-11-07
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Version: 4.3.0
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Date: 2022-11-18
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Title: Tools for Single Cell Genomics
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Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
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Authors@R: c(
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person(given = "Jeff", family = "Farrell", email = "[email protected]", role = "ctb"),
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person(given = "Christoph", family = "Hafemeister", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-6365-8254")),
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person(given = "Yuhan", family = "Hao", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-1810-0822")),
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person(given = "Austin", family = "Hartman", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-7278-1852")),
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person(given = "Paul", family = "Hoffman", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7693-8957")),
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person(given = "Jaison", family = "Jain", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-9478-5018")),
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person(given = "Madeline", family = "Kowalski", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-5655-7620")),
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person(given = "Efthymia", family = "Papalexi", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-5898-694X")),
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person(given = "Patrick", family = "Roelli", email = "[email protected]", role = "ctb"),
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person(given = "Rahul", family = "Satija", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-9448-8833")),
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pbapply,
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plotly (>= 4.9.0),
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png,
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progressr,
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RANN,
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RColorBrewer,
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Rcpp (>= 1.0.7),
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'tree.R'
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'utilities.R'
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'zzz.R'
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RoxygenNote: 7.2.1
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RoxygenNote: 7.2.2
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Encoding: UTF-8
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Suggests:
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ape,
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metap,
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enrichR,
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mixtools,
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ggrastr
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ggrastr,
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data.table,
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R.utils

‎NAMESPACE

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S3method(dim,STARmap)
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S3method(dim,SlideSeq)
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S3method(dim,VisiumV1)
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S3method(fortify,Centroids)
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S3method(fortify,Molecules)
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S3method(fortify,Segmentation)
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S3method(levels,SCTAssay)
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S3method(merge,SCTAssay)
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S3method(subset,AnchorSet)
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S3method(subset,SCTAssay)
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S3method(subset,STARmap)
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S3method(subset,SlideSeq)
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S3method(subset,VisiumV1)
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export("%iff%")
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export("%||%")
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export("DefaultAssay<-")
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export("Idents<-")
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export("Index<-")
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export(ISpatialDimPlot)
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export(ISpatialFeaturePlot)
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export(Idents)
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export(ImageDimPlot)
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export(ImageFeaturePlot)
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export(Images)
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export(Index)
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export(Indices)
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export(LinkedDimPlot)
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export(LinkedFeaturePlot)
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export(Load10X_Spatial)
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export(LoadAkoya)
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export(LoadAnnoyIndex)
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export(LoadHuBMAPCODEX)
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export(LoadNanostring)
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export(LoadSTARmap)
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export(LoadVizgen)
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export(LoadXenium)
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export(Loadings)
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export(LocalStruct)
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export(LogNormalize)
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export(Read10X)
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export(Read10X_Image)
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export(Read10X_h5)
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export(ReadAkoya)
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export(ReadMtx)
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export(ReadNanostring)
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export(ReadParseBio)
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export(ReadSTARsolo)
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export(ReadSlideSeq)
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export(ReadVitessce)
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export(ReadVizgen)
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export(ReadXenium)
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export(Reductions)
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export(RegroupIdents)
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export(RelativeCounts)
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export(SingleDimPlot)
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export(SingleExIPlot)
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export(SingleImageMap)
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export(SingleImagePlot)
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export(SingleRasterMap)
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export(SingleSpatialPlot)
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export(SpatialDimPlot)
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importFrom(RcppAnnoy,AnnoyHamming)
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importFrom(RcppAnnoy,AnnoyManhattan)
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importFrom(Rtsne,Rtsne)
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importFrom(SeuratObject,"%!NA%")
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importFrom(SeuratObject,"%NA%")
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importFrom(SeuratObject,"%iff%")
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importFrom(SeuratObject,"%||%")
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importFrom(SeuratObject,"DefaultAssay<-")
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importFrom(SeuratObject,"Idents<-")
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importFrom(SeuratObject,"Index<-")
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importFrom(SeuratObject,"VariableFeatures<-")
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importFrom(SeuratObject,AddMetaData)
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importFrom(SeuratObject,Assays)
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importFrom(SeuratObject,AttachDeps)
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importFrom(SeuratObject,Boundaries)
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importFrom(SeuratObject,Cells)
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importFrom(SeuratObject,CellsByIdentities)
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importFrom(SeuratObject,Command)
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importFrom(SeuratObject,CreateAssayObject)
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importFrom(SeuratObject,CreateCentroids)
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importFrom(SeuratObject,CreateDimReducObject)
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importFrom(SeuratObject,CreateFOV)
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importFrom(SeuratObject,CreateSegmentation)
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importFrom(SeuratObject,CreateSeuratObject)
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importFrom(SeuratObject,DefaultAssay)
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importFrom(SeuratObject,DefaultBoundary)
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importFrom(SeuratObject,DefaultDimReduc)
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importFrom(SeuratObject,DefaultFOV)
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importFrom(SeuratObject,Distances)
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importFrom(SeuratObject,Embeddings)
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importFrom(SeuratObject,Features)
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importFrom(SeuratObject,FetchData)
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importFrom(SeuratObject,GetAssayData)
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importFrom(SeuratObject,GetImage)
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importFrom(SeuratObject,IsGlobal)
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importFrom(SeuratObject,JS)
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importFrom(SeuratObject,Key)
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importFrom(SeuratObject,Keys)
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importFrom(SeuratObject,Loadings)
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importFrom(SeuratObject,LogSeuratCommand)
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importFrom(SeuratObject,Misc)
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importFrom(SeuratObject,Molecules)
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importFrom(SeuratObject,Neighbors)
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importFrom(SeuratObject,Overlay)
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importFrom(SeuratObject,PackageCheck)
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importFrom(SeuratObject,Project)
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importFrom(SeuratObject,Radius)
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importFrom(ggplot2,element_text)
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importFrom(ggplot2,facet_grid)
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importFrom(ggplot2,facet_wrap)
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importFrom(ggplot2,fortify)
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importFrom(ggplot2,geom_abline)
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importFrom(ggplot2,geom_bar)
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importFrom(ggplot2,geom_blank)
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importFrom(ggplot2,position_dodge)
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importFrom(ggplot2,position_jitterdodge)
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importFrom(ggplot2,scale_alpha)
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importFrom(ggplot2,scale_alpha_manual)
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importFrom(ggplot2,scale_alpha_ordinal)
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importFrom(ggplot2,scale_color_brewer)
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importFrom(ggplot2,scale_color_distiller)
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importFrom(igraph,plot.igraph)
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importFrom(irlba,irlba)
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importFrom(jsonlite,fromJSON)
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importFrom(jsonlite,read_json)
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importFrom(leiden,leiden)
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importFrom(lmtest,lrtest)
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importFrom(matrixStats,rowAnyNAs)
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importFrom(methods,"slot<-")
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importFrom(methods,.hasSlot)
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importFrom(methods,as)
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importFrom(methods,getMethod)
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importFrom(methods,is)
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importFrom(methods,new)
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importFrom(methods,setAs)
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importFrom(methods,setClass)
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importFrom(methods,setClassUnion)
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importFrom(methods,setGeneric)
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importFrom(methods,setMethod)
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importFrom(methods,setOldClass)
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importFrom(methods,setValidity)
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importFrom(plotly,plot_ly)
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importFrom(plotly,raster2uri)
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importFrom(png,readPNG)
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importFrom(progressr,progressor)
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importFrom(reticulate,import)
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importFrom(reticulate,py_module_available)
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importFrom(reticulate,py_set_seed)
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importFrom(rlang,"!!")
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importFrom(rlang,as_label)
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importFrom(rlang,invoke)
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importFrom(rlang,is_na)
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importFrom(rlang,sym)
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importFrom(scales,brewer_pal)
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importFrom(scales,hue_pal)
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importFrom(scales,rescale)
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importFrom(stats,wilcox.test)
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importFrom(tibble,tibble)
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importFrom(tools,file_ext)
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importFrom(tools,file_path_sans_ext)
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importFrom(utils,argsAnywhere)
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importFrom(utils,capture.output)
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importFrom(utils,file_test)

‎NEWS.md

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# Seurat 4.2.1 (2022-11-07)
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# Seurat 4.3.0 (2022-11-18)
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## Added
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- Add support for imaging-based spatial datasets
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## Changes
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- Fix bug in `FindMarkers()` when run post Integration/Transfer ([#6856](https://github.com/satijalab/seurat/issues/6586))
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# Seurat 4.2.1 (2022-11-08)
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## Changes
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- Replaced import from `spatstat.core` with `spatstat.explore`

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