KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Software and Algorithms
Fiji ImageJ	NA	https://imagej.net/software/fiji/
QuPath	NA	https://qupath.github.io/
MGI	NA	https://www.informatics.jax.org/vocab/gene_ontology/
Seurat	R Package	https://satijalab.org/seurat/
kallisto | bustools	Pachter Lab	https://www.kallistobus.tools/
DropletUtils	R Package	https://bioconductor.org/packages/release/bioc/html/DropletUtils.html
Illustrator	Adobe	https://www.adobe.com/illustrator
SoupX	R Package	https://cran.r-project.org/web/packages/SoupX/index.html
BUSpaRse	R Package	https://bioconductor.org/packages/release/bioc/html/BUSpaRse.html
kit	R Package	https://cran.r-project.org/web/packages/kit/index.html
tidyverse	R Package	https://cran.r-project.org/web/packages/tidyverse/index.html
stringr	R Package	https://cran.r-project.org/web/packages/stringr/index.html
clustree	R Package	https://cran.r-project.org/web/packages/clustree/index.html
ggplot2	R Package	https://cran.r-project.org/web/packages/ggplot2/index.html
data.table	R Package	https://cran.r-project.org/web/packages/data.table/index.html
org.Mm.eg.db	R Package	https://bioconductor.org/packages/release/data/annotation/html/org.Mm.eg.db.html
dplyr	R Package	https://cran.r-project.org/web/packages/dplyr/index.html
DBI	R Package	https://cran.r-project.org/web/packages/DBI/index.html
glmGamPoi	R Package	https://bioconductor.org/packages/release/bioc/html/glmGamPoi.html
ggpubr	R Package	https://cran.r-project.org/web/packages/ggpubr/index.html
svglite	R Package	https://cran.r-project.org/web/packages/svglite/index.html
vegan	R Package	https://cran.r-project.org/web/packages/vegan/index.html
scales	R Package	https://cran.r-project.org/web/packages/scales/index.html
Scrublet	Python Package	https://github.com/swolock/scrublet
reticulate	R Package	https://cran.r-project.org/web/packages/reticulate/index.html
plotly	R Package	https://plotly.com/r/
Matrix	R Package	https://cran.r-project.org/web/packages/Matrix/index.html
tibble	R Package	https://cran.r-project.org/web/packages/tibble/index.html
stats	R Package	https://stat.ethz.ch/R-manual/R-devel/library/stats/html/00Index.html
patchwork	R Package	https://cran.r-project.org/web/packages/patchwork/index.html
openxlsx	R Package	https://cran.r-project.org/web/packages/openxlsx/index.html
gridExtra	R Package	https://cran.r-project.org/web/packages/gridExtra/index.html
ggrepel	R Package	https://cran.r-project.org/web/packages/ggrepel/index.html
GeneOverlap	R Package	https://bioconductor.org/packages/release/bioc/html/GeneOverlap.html
biomaRt	R Package	https://bioconductor.org/packages/release/bioc/html/biomaRt.html
circlize	R Package	https://cran.r-project.org/web/packages/circlize/index.html
slingshot	R Package	https://www.bioconductor.org/packages/release/bioc/html/slingshot.html
tradeSeq	R Package	https://www.bioconductor.org/packages/release/bioc/html/tradeSeq.html
SingleCellExperiment	R Package	https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html
viridis	R Package	https://cran.r-project.org/web/packages/viridis/index.html
pheatmap	R Package	https://cran.r-project.org/web/packages/pheatmap/index.html
msigdbr	R Package	https://cran.r-project.org/web/packages/msigdbr/vignettes/msigdbr-intro.html
fgsea	R Package	https://bioconductor.org/packages/release/bioc/html/fgsea.html
IDPmisc	R Package	https://cran.r-project.org/web/packages/IDPmisc/index.html
msa	R Package	https://bioconductor.org/packages/release/bioc/html/msa.html
ggpointdensity	R Package	https://cran.r-project.org/web/packages/ggpointdensity/index.html
eulerr	R Package	https://cran.r-project.org/web/packages/eulerr/index.html
seqinr	R Package	https://cran.r-project.org/web/packages/seqinr/index.html
geomtextpath	R Package	https://cran.r-project.org/web/packages/geomtextpath/index.html
Rmisc	R Package	https://cran.r-project.org/web/packages/Rmisc/index.html
ggplotify	R Package	https://cran.r-project.org/web/packages/ggplotify/index.html
Spatial Transcriptomics
Molecular Cartography©	Resolve Biosciences	https://resolvebiosciences.com/