Package: Spaniel 1.27.0

Rachel Queen

Spaniel: Spatial Transcriptomics Analysis

Spaniel includes a series of tools to aid the quality control and analysis of Spatial Transcriptomics data. Spaniel can import data from either the original Spatial Transcriptomics system or 10X Visium technology. The package contains functions to create a SingleCellExperiment Seurat object and provides a method of loading a histologial image into R. The spanielPlot function allows visualisation of metrics contained within the S4 object overlaid onto the image of the tissue.

Authors:Rachel Queen [aut, cre]

Spaniel_1.27.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Spaniel/json (API)

# Install 'Spaniel' in R:

install.packages('Spaniel', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:Spaniel-1.27.0(bioc 3.24)Spaniel-1.26.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

singlecell rnaseq qualitycontrol preprocessing normalization visualization transcriptomics geneexpression sequencing software dataimport datarepresentation infrastructure coverage clustering

4.54 score 35 scripts 10 exports 197 dependencies

Last updated from:c4e09da6d7. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	246
linux-devel-x86_64	NOTE	423
source / vignettes	OK	402
linux-release-x86_64	NOTE	493
macos-release-arm64	NOTE	231
macos-oldrel-arm64	NOTE	254
windows-devel	NOTE	314
windows-release	NOTE	332
windows-oldrel	NOTE	317
wasm-release	OK	251

Exports:addCoordinates createSCE createSeurat createVisiumSCE markClusterCol parseImage removeSpots runShinySpaniel selectSpots spanielPlot

Dependencies:abind askpass assorthead base64enc beachmat beeswarm BH Biobase BiocGenerics biocmake BiocNeighbors BiocParallel BiocSingular bitops bluster bslib cachem caTools cli cluster codetools commonmark cowplot cpp11 crosstalk curl data.table DelayedArray DelayedMatrixStats deldir digest dir.expiry dotCall64 dplyr dqrng DropletUtils edgeR evaluate farver fastDummies fastmap filelock fitdistrplus FNN fontawesome formatR fs futile.logger futile.options future future.apply generics GenomicRanges ggbeeswarm ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools h5mread HDF5Array here highr htmltools htmlwidgets httpuv httr ica igraph IRanges irlba isoband jpeg jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma listenv lmtest locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise metapod mime miniUI nlme openssl otel parallelly patchwork pbapply pheatmap pillar pkgconfig plotly plyr png polyclip progressr promises purrr R.methodsS3 R.oo R.utils R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppML RcppProgress RcppTOML reshape2 reticulate rhdf5 rhdf5filters Rhdf5lib rlang rmarkdown ROCR rprojroot RSpectra rsvd Rtsne S4Arrays S4Vectors S7 sass ScaledMatrix scales scater scattermore scran sctransform scuttle Seqinfo Seurat SeuratObject shiny SingleCellExperiment sitmo snow sourcetools sp spam SparseArray sparseMatrixStats spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils statmod stringi stringr SummarizedExperiment survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs vipor viridis viridisLite withr xfun xtable XVector yaml zoo

Spaniel 10X Visium

Rendered fromspaniel-vignette-tenX-import.Rmdusingknitr::rmarkdown

Last update: 2021-05-13
Started: 2021-05-11

Help page	Topics
Add coordinates to Object Adds output of Spot Detector coordinates to Seurat object or SCE object created by createSeurat/createSCE. Details about how to use Spot Detector can be found: https://github.com/SpatialTranscriptomicsResearch/st_spot_detector	addCoordinates
Create a SingleCellExperiment Object From Spatial Transcriptomics Data	createSCE
Create a Seurat Object From Spatial Transcriptomics Data	createSeurat
createVisiumSCE	createVisiumSCE
markClusterCol	markClusterCol
This function parses a HE image to use as the background for plots	parseImage
removeSpots	removeSpots
RunShinySpaniel	runShinySpaniel
selectSpots	selectSpots
Spatial Transcriptomics Plot	spanielPlot

Package: Spaniel 1.27.0

Spaniel: Spatial Transcriptomics Analysis

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Help Manual

Usage by other packages (reverse dependencies)