Package: SpotSweeper 1.1.0

Michael Totty

SpotSweeper: Spatially-aware quality control for spatial transcriptomics

Spatially-aware quality control (QC) software for both spot-level and artifact-level QC in spot-based spatial transcripomics, such as 10x Visium. These methods calculate local (nearest-neighbors) mean and variance of standard QC metrics (library size, unique genes, and mitochondrial percentage) to identify outliers spot and large technical artifacts. Scales linearly with the number of spots and is designed to be used with 'SpatialExperiment' objects.

Authors:Michael Totty [aut, cre], Boyi Guo [aut]

SpotSweeper_1.1.0.tar.gz
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SpotSweeper_1.1.0.tgz(r-4.4-any)SpotSweeper_1.1.0.tgz(r-4.3-any)
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SpotSweeper.pdf |SpotSweeper.html✨
SpotSweeper/json (API)
NEWS

# Install 'SpotSweeper' in R:

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

Bug tracker:https://github.com/mictott/spotsweeper/issues

Datasets:

DLPFC_artifact - Human DLPFC dataset with a technical artifact (hangnail).

On BioConductor:SpotSweeper-1.1.0(bioc 3.20)SpotSweeper-1.0.0(bioc 3.19)

bioconductor-package

5 exports 1.69 score 100 dependencies

Last updated 2 months agofrom:1879e1ee6c

Exports:findArtifacts localOutliers localVariance plotQC plotQCpdf

Dependencies:abind askpass BH Biobase BiocFileCache BiocGenerics BiocNeighbors BiocParallel bit bit64 blob cachem class classInt cli codetools colorspace cpp11 crayon curl DBI dbplyr DelayedArray dplyr e1071 escheR fansi farver fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite KernSmooth labeling lambda.r lattice lifecycle magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr proxy purrr R6 RColorBrewer Rcpp RcppHNSW rjson rlang RSQLite s2 S4Arrays S4Vectors scales sf SingleCellExperiment snow SparseArray spatialEco SpatialExperiment stringi stringr SummarizedExperiment sys terra tibble tidyr tidyselect UCSC.utils units utf8 vctrs viridisLite withr wk XVector zlibbioc

Getting started with 'SpotSweeper'

Michael Totty, Boyi Guo, Stephanie Hicks

Rendered fromgetting_started.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2024-04-10
Started: 2024-02-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
human DLPFC dataset with a technical artifact (hangnail).	DLPFC_artifact
Identify and annotate artifacts in spatial transcriptomics data	findArtifacts
localOutliers Function	localOutliers
localVariance Function	localVariance
Plot QC metrics for a Single Sample in a SpatialExperiment object	plotQC
Plot Outlier Metrics to PDF	plotQCpdf