Package: SpotSweeper 1.3.2

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.

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

SpotSweeper_1.3.2.tar.gz
SpotSweeper_1.3.2.zip(r-4.5)SpotSweeper_1.3.2.zip(r-4.4)SpotSweeper_1.3.0.zip(r-4.3)
SpotSweeper_1.3.2.tgz(r-4.4-any)SpotSweeper_1.3.0.tgz(r-4.3-any)
SpotSweeper_1.3.2.tar.gz(r-4.5-noble)SpotSweeper_1.3.2.tar.gz(r-4.4-noble)
SpotSweeper_1.3.2.tgz(r-4.4-emscripten)SpotSweeper_1.3.0.tgz(r-4.3-emscripten)
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).
biased_spots - Biased Spots Data

On BioConductor:SpotSweeper-1.3.2(bioc 3.21)SpotSweeper-1.2.0(bioc 3.20)

software spatial transcriptomics qualitycontrol geneexpression bioconductor quality-control spatial-transcriptomics

6.79 score 5 stars 65 scripts 168 downloads 6 exports 100 dependencies

Last updated 14 days agofrom:9f16259b96. Checks:OK: 1 NOTE: 4 ERROR: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 04 2024
R-4.5-win	NOTE	Dec 04 2024
R-4.5-linux	NOTE	Dec 04 2024
R-4.4-win	NOTE	Dec 04 2024
R-4.4-mac	NOTE	Dec 04 2024
R-4.3-win	ERROR	Nov 30 2024
R-4.3-mac	ERROR	Nov 30 2024

Exports:findArtifacts flagVisiumOutliers localOutliers localVariance plotQCmetrics plotQCpdf

Dependencies:abind askpass assorthead 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 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 Dec 04 2024.

Last update: 2024-11-08
Started: 2024-02-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Biased Spots Data	biased_spots
human DLPFC dataset with a technical artifact (hangnail).	DLPFC_artifact
Identify and annotate artifacts in spatial transcriptomics data	findArtifacts
Flag Visium Outliers in SpatialExperiment Objects	flagVisiumOutliers
localOutliers Function	localOutliers
localVariance Function	localVariance
Plot QC metrics for a Single Sample in a SpatialExperiment object	plotQCmetrics
Plot Outlier Metrics to PDF	plotQCpdf