6 Wrap up
There are a lot more things one can do with the data, and what we’ve done here is just the beginning. Many new exciting tools for performing analyses of spatial omic data are being developed as we speak. What further defines these clusters that we just generated? How are some cells behaving depending on their spatial context? What will we learn if we integrate our data with scRNA-seq or other spatial omic data? Go out and explore!
This analysis was last compiled on 2022-04-29.
::session_info() devtools
## ─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.1.3 (2022-03-10)
## os macOS Monterey 12.3.1
## system x86_64, darwin13.4.0
## ui RStudio
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Europe/Stockholm
## date 2022-04-29
## rstudio 2022.02.1+461 Prairie Trillium (desktop)
## pandoc 2.18 @ /Users/ludviglarsson/anaconda3/envs/R4.1/bin/ (via rmarkdown)
##
## ─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## abind 1.4-5 2016-07-21 [1] CRAN (R 4.1.3)
## akima 0.6-3.3 2022-04-19 [1] CRAN (R 4.1.3)
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## beachmat 2.10.0 2021-10-26 [1] Bioconductor
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## Biobase * 2.54.0 2021-10-26 [1] Bioconductor
## BiocGenerics * 0.40.0 2021-10-26 [1] Bioconductor
## BiocManager 1.30.16 2021-06-15 [1] CRAN (R 4.1.3)
## BiocParallel 1.28.3 2021-12-09 [1] Bioconductor
## BioQC * 1.22.0 2021-10-26 [1] Bioconductor
## bit 4.0.4 2020-08-04 [1] CRAN (R 4.1.0)
## bit64 4.0.5 2020-08-30 [1] CRAN (R 4.1.0)
## bitops 1.0-7 2021-04-24 [1] CRAN (R 4.1.0)
## bmp 0.3 2017-09-11 [1] CRAN (R 4.1.3)
## bookdown 0.26 2022-04-15 [1] CRAN (R 4.1.3)
## boot 1.3-28 2021-05-03 [1] CRAN (R 4.1.0)
## brio 1.1.3 2021-11-30 [1] CRAN (R 4.1.1)
## bslib 0.3.1 2021-10-06 [1] CRAN (R 4.1.1)
## cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.1)
## callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.0)
## class 7.3-20 2022-01-13 [1] CRAN (R 4.1.2)
## classInt 0.4-3 2020-04-07 [1] CRAN (R 4.1.0)
## cli 3.2.0 2022-02-14 [1] CRAN (R 4.1.2)
## cluster 2.1.3 2022-03-28 [1] CRAN (R 4.1.2)
## codetools 0.2-18 2020-11-04 [1] CRAN (R 4.1.0)
## colorRamps 2.3 2012-10-29 [1] CRAN (R 4.1.3)
## colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.1.2)
## cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.1.3)
## crayon 1.5.1 2022-03-26 [1] CRAN (R 4.1.2)
## crosstalk 1.2.0 2021-11-04 [1] CRAN (R 4.1.1)
## data.table 1.14.2 2021-09-27 [1] CRAN (R 4.1.1)
## DBI 1.1.2 2021-12-20 [1] CRAN (R 4.1.2)
## dbscan 1.1-10 2022-01-15 [1] CRAN (R 4.1.3)
## DelayedArray 0.20.0 2021-10-26 [1] Bioconductor
## DelayedMatrixStats 1.16.0 2021-10-26 [1] Bioconductor
## deldir 1.0-6 2021-10-23 [1] CRAN (R 4.1.1)
## desc 1.4.1 2022-03-06 [1] CRAN (R 4.1.2)
## devtools 2.4.3 2021-11-30 [1] CRAN (R 4.1.1)
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## doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.1.3)
## dplyr * 1.0.8 2022-02-08 [1] CRAN (R 4.1.2)
## DT * 0.22 2022-03-28 [1] CRAN (R 4.1.2)
## e1071 1.7-9 2021-09-16 [1] CRAN (R 4.1.1)
## edgeR 3.36.0 2021-10-26 [1] Bioconductor
## ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
## evaluate 0.15 2022-02-18 [1] CRAN (R 4.1.2)
## fansi 1.0.3 2022-03-24 [1] CRAN (R 4.1.2)
## farver 2.1.0 2021-02-28 [1] CRAN (R 4.1.0)
## fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0)
## fitdistrplus 1.1-8 2022-03-10 [1] CRAN (R 4.1.3)
## foreach 1.5.2 2022-02-02 [1] CRAN (R 4.1.2)
## fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.3)
## future 1.24.0 2022-02-19 [1] CRAN (R 4.1.2)
## future.apply 1.8.1 2021-08-10 [1] CRAN (R 4.1.1)
## generics 0.1.2 2022-01-31 [1] CRAN (R 4.1.2)
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## GGally * 2.1.2 2021-06-21 [1] CRAN (R 4.1.3)
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## ggridges 0.5.3 2021-01-08 [1] CRAN (R 4.1.3)
## globals 0.14.0 2020-11-22 [1] CRAN (R 4.1.0)
## glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.2)
## goftest 1.2-3 2021-10-07 [1] CRAN (R 4.1.3)
## gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.3)
## gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0)
## harmony * 0.1.0 2021-06-02 [1] CRAN (R 4.1.3)
## hdf5r 1.3.5 2021-11-15 [1] CRAN (R 4.1.1)
## highr 0.9 2021-04-16 [1] CRAN (R 4.1.0)
## hms 1.1.1 2021-09-26 [1] CRAN (R 4.1.1)
## htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.1)
## htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.1.1)
## httpuv 1.6.5 2022-01-05 [1] CRAN (R 4.1.2)
## httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.0)
## ica 1.0-2 2018-05-24 [1] CRAN (R 4.1.3)
## igraph 1.3.0 2022-04-01 [1] CRAN (R 4.1.3)
## imager 0.42.13 2022-03-07 [1] CRAN (R 4.1.3)
## IRanges * 2.28.0 2021-10-26 [1] Bioconductor
## irlba 2.3.5 2021-12-06 [1] CRAN (R 4.1.3)
## iterators 1.0.14 2022-02-05 [1] CRAN (R 4.1.2)
## jpeg 0.1-9 2021-07-24 [1] CRAN (R 4.1.3)
## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.1.0)
## jsonlite 1.8.0 2022-02-22 [1] CRAN (R 4.1.2)
## KernSmooth 2.23-20 2021-05-03 [1] CRAN (R 4.1.0)
## knitr 1.38 2022-03-25 [1] CRAN (R 4.1.2)
## labeling 0.4.2 2020-10-20 [1] CRAN (R 4.1.2)
## later 1.3.0 2021-08-18 [1] CRAN (R 4.1.3)
## lattice 0.20-45 2021-09-22 [1] CRAN (R 4.1.1)
## lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.0)
## leiden 0.3.9 2021-07-27 [1] CRAN (R 4.1.3)
## lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.1)
## limma 3.50.3 2022-04-07 [1] Bioconductor
## listenv 0.8.0 2019-12-05 [1] CRAN (R 4.1.0)
## lmtest 0.9-40 2022-03-21 [1] CRAN (R 4.1.3)
## locfit 1.5-9.5 2022-03-03 [1] CRAN (R 4.1.3)
## magick 2.7.3 2021-08-18 [1] CRAN (R 4.1.3)
## magrittr * 2.0.3 2022-03-30 [1] CRAN (R 4.1.3)
## MASS 7.3-56 2022-03-23 [1] CRAN (R 4.1.2)
## Matrix 1.4-1 2022-03-23 [1] CRAN (R 4.1.2)
## MatrixGenerics * 1.6.0 2021-10-26 [1] Bioconductor
## matrixStats * 0.62.0 2022-04-19 [1] CRAN (R 4.1.3)
## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.1.1)
## mgcv 1.8-40 2022-03-29 [1] CRAN (R 4.1.3)
## mime 0.12 2021-09-28 [1] CRAN (R 4.1.1)
## miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.1.0)
## Morpho 2.9 2021-09-09 [1] CRAN (R 4.1.3)
## munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.2)
## nlme 3.1-157 2022-03-25 [1] CRAN (R 4.1.2)
## NNLM * 0.4.4 2022-04-20 [1] Github (linxihui/NNLM@4574bca)
## openxlsx 4.2.5 2021-12-14 [1] CRAN (R 4.1.3)
## parallelly 1.31.0 2022-04-07 [1] CRAN (R 4.1.3)
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## pbapply 1.5-0 2021-09-16 [1] CRAN (R 4.1.3)
## pheatmap 1.0.12 2019-01-04 [1] CRAN (R 4.1.3)
## pillar 1.7.0 2022-02-01 [1] CRAN (R 4.1.2)
## pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.1.2)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
## pkgload 1.2.4 2021-11-30 [1] CRAN (R 4.1.1)
## plotly 4.10.0 2021-10-09 [1] CRAN (R 4.1.3)
## plyr 1.8.7 2022-03-24 [1] CRAN (R 4.1.2)
## png 0.1-7 2013-12-03 [1] CRAN (R 4.1.3)
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## prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0)
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## purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0)
## R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.1)
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## raster 3.5-15 2022-01-22 [1] CRAN (R 4.1.2)
## RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.1.3)
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##
## [1] /Users/ludviglarsson/anaconda3/envs/R4.1/lib/R/library
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