This is an R Markdown website, created by Julia Wrobel for a single-cell spatial proteomics and multiplex imaging data workshop at the 2024 Pacific Symposium on Biocomputing (PSB). For raw materials, go to the GitHub repository for this website.
In the short course, we will use several packages which are listed below. Code to install the packages follows, and version information about each of these packages and their dependencies is at the bottom of this page.
Installing packages from CRAN
# main packages
install.packages(c("tidyverse", "spatstat", "spatialTIME", "mxnorm","survival", "scSpatialSim"))
# additional packages used for visualization
install.packages(c("viridis", "patchwork"))Installing packages from GitHub
# install devtools
install.packages("devtools")
# mxfda
devtools::install_github("julia-wrobel/mxfda")Installing packages from Bioconductor
# install Bioconductor
BiocManager::install(version = "3.16")
# VectraPolarisData
BiocManager::install("VectraPolarisData")Versions of key packages:
devtools::session_info(c("tidyverse", "VectraPolarisData", "spatstat", "spatialTIME", "mxfda"))## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.3.1 (2023-06-16)
## os macOS Sonoma 14.1.1
## system aarch64, darwin20
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Europe/Berlin
## date 2023-12-20
## pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.0)
## AnnotationDbi 1.62.2 2023-07-02 [1] Bioconductor
## AnnotationHub 3.8.0 2023-05-08 [1] Bioconductor
## ash 1.0-15 2015-09-01 [1] CRAN (R 4.3.0)
## askpass 1.2.0 2023-09-03 [1] CRAN (R 4.3.0)
## backports 1.4.1 2021-12-13 [1] CRAN (R 4.3.0)
## base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.3.0)
## beachmat 2.16.0 2023-05-08 [1] Bioconductor
## BH 1.81.0-1 2023-01-22 [1] CRAN (R 4.3.0)
## Biobase 2.60.0 2023-05-08 [1] Bioconductor
## BiocFileCache 2.8.0 2023-05-08 [1] Bioconductor
## BiocGenerics 0.46.0 2023-06-04 [1] Bioconductor
## BiocManager 1.30.22 2023-08-08 [1] CRAN (R 4.3.0)
## BiocParallel 1.34.2 2023-05-28 [1] Bioconductor
## BiocVersion 3.17.1 2022-12-20 [1] Bioconductor
## Biostrings 2.68.1 2023-05-21 [1] Bioconductor
## bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0)
## bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0)
## bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0)
## blob 1.2.4 2023-03-17 [1] CRAN (R 4.3.0)
## boot 1.3-28.1 2022-11-22 [1] CRAN (R 4.3.1)
## brio 1.1.3 2021-11-30 [1] CRAN (R 4.3.0)
## broom 1.0.5 2023-06-09 [1] CRAN (R 4.3.0)
## bslib 0.5.1 2023-08-11 [1] CRAN (R 4.3.0)
## cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0)
## callr 3.7.3 2022-11-02 [1] CRAN (R 4.3.0)
## cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.3.0)
## cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0)
## clipr 0.8.0 2022-02-22 [1] CRAN (R 4.3.0)
## cluster 2.1.4 2022-08-22 [1] CRAN (R 4.3.1)
## codetools 0.2-19 2023-02-01 [1] CRAN (R 4.3.1)
## colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0)
## commonmark 1.9.0 2023-03-17 [1] CRAN (R 4.3.0)
## conflicted 1.2.0 2023-02-01 [1] CRAN (R 4.3.0)
## cpp11 0.4.7 2023-12-02 [1] CRAN (R 4.3.1)
## crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0)
## crosstalk 1.2.0 2021-11-04 [1] CRAN (R 4.3.0)
## curl 5.0.2 2023-08-14 [1] CRAN (R 4.3.0)
## data.table 1.14.8 2023-02-17 [1] CRAN (R 4.3.0)
## DBI 1.1.3 2022-06-18 [1] CRAN (R 4.3.0)
## dbplyr 2.3.4 2023-09-26 [1] CRAN (R 4.3.1)
## DelayedArray 0.26.7 2023-07-30 [1] Bioconductor
## DelayedMatrixStats 1.22.6 2023-09-03 [1] Bioconductor
## deldir 2.0-2 2023-11-23 [1] CRAN (R 4.3.1)
## desc 1.4.2 2022-09-08 [1] CRAN (R 4.3.0)
## deSolve 1.40 2023-11-27 [1] CRAN (R 4.3.1)
## diffobj 0.3.5 2021-10-05 [1] CRAN (R 4.3.0)
## digest 0.6.33 2023-07-07 [1] CRAN (R 4.3.0)
## dixon 0.0-8 2022-02-12 [1] CRAN (R 4.3.0)
## dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.3.1)
## dqrng 0.3.1 2023-08-30 [1] CRAN (R 4.3.0)
## DropletUtils 1.20.0 2023-05-08 [1] Bioconductor
## DT 0.29 2023-08-29 [1] CRAN (R 4.3.0)
## dtplyr 1.3.1 2023-03-22 [1] CRAN (R 4.3.0)
## edgeR 3.42.4 2023-06-04 [1] Bioconductor
## ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
## evaluate 0.23 2023-11-01 [1] CRAN (R 4.3.1)
## ExperimentHub 2.8.1 2023-07-16 [1] Bioconductor
## fansi 1.0.5 2023-10-08 [1] CRAN (R 4.3.1)
## farver 2.1.1 2022-07-06 [1] CRAN (R 4.3.0)
## fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
## fda 6.1.4 2023-05-23 [1] CRAN (R 4.3.0)
## fds 1.8 2018-10-31 [1] CRAN (R 4.3.0)
## filelock 1.0.2 2018-10-05 [1] CRAN (R 4.3.0)
## FNN 1.1.3.2 2023-03-20 [1] CRAN (R 4.3.0)
## fontawesome 0.5.2 2023-08-19 [1] CRAN (R 4.3.0)
## forcats 1.0.0 2023-01-29 [1] CRAN (R 4.3.0)
## formatR 1.14 2023-01-17 [1] CRAN (R 4.3.0)
## fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.0)
## furrr 0.3.1 2022-08-15 [1] CRAN (R 4.3.0)
## futile.logger 1.4.3 2016-07-10 [1] CRAN (R 4.3.0)
## futile.options 1.0.1 2018-04-20 [1] CRAN (R 4.3.0)
## future 1.33.0 2023-07-01 [1] CRAN (R 4.3.0)
## gamm4 0.2-6 2020-04-03 [1] CRAN (R 4.3.0)
## gargle 1.5.2 2023-07-20 [1] CRAN (R 4.3.0)
## generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
## GenomeInfoDb 1.36.3 2023-09-10 [1] Bioconductor
## GenomeInfoDbData 1.2.10 2023-08-04 [1] Bioconductor
## GenomicRanges 1.52.0 2023-05-08 [1] Bioconductor
## ggplot2 3.4.4 2023-10-12 [1] CRAN (R 4.3.1)
## globals 0.16.2 2022-11-21 [1] CRAN (R 4.3.0)
## glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0)
## goftest 1.2-3 2021-10-07 [1] CRAN (R 4.3.0)
## googledrive 2.1.1 2023-06-11 [1] CRAN (R 4.3.0)
## googlesheets4 1.1.1 2023-06-11 [1] CRAN (R 4.3.0)
## grpreg 3.4.0 2021-07-26 [1] CRAN (R 4.3.0)
## gtable 0.3.4 2023-08-21 [1] CRAN (R 4.3.0)
## haven 2.5.3 2023-06-30 [1] CRAN (R 4.3.0)
## HDF5Array 1.28.1 2023-05-08 [1] Bioconductor
## hdrcde 3.4 2021-01-18 [1] CRAN (R 4.3.0)
## highr 0.10 2022-12-22 [1] CRAN (R 4.3.0)
## hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0)
## htmltools 0.5.6 2023-08-10 [1] CRAN (R 4.3.0)
## htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.3.0)
## httpuv 1.6.11 2023-05-11 [1] CRAN (R 4.3.0)
## httr 1.4.7 2023-08-15 [1] CRAN (R 4.3.0)
## ids 1.0.1 2017-05-31 [1] CRAN (R 4.3.0)
## interactiveDisplayBase 1.38.0 2023-05-08 [1] Bioconductor
## IRanges 2.34.1 2023-07-02 [1] Bioconductor
## isoband 0.2.7 2022-12-20 [1] CRAN (R 4.3.0)
## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.3.0)
## jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.3.1)
## KEGGREST 1.40.0 2023-05-08 [1] Bioconductor
## kernlab 0.9-32 2023-01-31 [1] CRAN (R 4.3.0)
## KernSmooth 2.23-22 2023-07-10 [1] CRAN (R 4.3.0)
## knitr 1.44 2023-09-11 [1] CRAN (R 4.3.0)
## ks 1.14.1 2023-08-10 [1] CRAN (R 4.3.0)
## labeling 0.4.3 2023-08-29 [1] CRAN (R 4.3.0)
## lambda.r 1.2.4 2019-09-18 [1] CRAN (R 4.3.0)
## later 1.3.1 2023-05-02 [1] CRAN (R 4.3.0)
## lattice 0.21-8 2023-04-05 [1] CRAN (R 4.3.1)
## lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.3.0)
## lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.1)
## limma 3.56.2 2023-06-04 [1] Bioconductor
## listenv 0.9.0 2022-12-16 [1] CRAN (R 4.3.0)
## lme4 1.1-35.1 2023-11-05 [1] CRAN (R 4.3.1)
## locfit 1.5-9.8 2023-06-11 [1] CRAN (R 4.3.0)
## lubridate 1.9.3 2023-09-27 [1] CRAN (R 4.3.1)
## magic 1.6-1 2022-11-16 [1] CRAN (R 4.3.0)
## magick 2.8.0 2023-09-25 [1] CRAN (R 4.3.1)
## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
## MASS 7.3-60 2023-05-04 [1] CRAN (R 4.3.1)
## Matrix 1.6-1.1 2023-09-18 [1] CRAN (R 4.3.1)
## MatrixGenerics 1.12.3 2023-07-30 [1] Bioconductor
## matrixStats 1.0.0 2023-06-02 [1] CRAN (R 4.3.0)
## mclust 6.0.1 2023-11-15 [1] CRAN (R 4.3.1)
## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0)
## mgcv 1.9-0 2023-07-11 [1] CRAN (R 4.3.0)
## mime 0.12 2021-09-28 [1] CRAN (R 4.3.0)
## minqa 1.2.6 2023-09-11 [1] CRAN (R 4.3.0)
## misc3d 0.9-1 2021-10-07 [1] CRAN (R 4.3.0)
## modelr 0.1.11 2023-03-22 [1] CRAN (R 4.3.0)
## multicool 1.0.0 2023-12-02 [1] CRAN (R 4.3.1)
## munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0)
## mvtnorm 1.2-4 2023-11-27 [1] CRAN (R 4.3.1)
## mxfda 0.1.0 2023-12-07 [1] local
## nlme 3.1-163 2023-08-09 [1] CRAN (R 4.3.0)
## nloptr 2.0.3 2022-05-26 [1] CRAN (R 4.3.0)
## openssl 2.1.1 2023-09-25 [1] CRAN (R 4.3.1)
## parallelly 1.36.0 2023-05-26 [1] CRAN (R 4.3.0)
## pbmcapply 1.5.1 2022-04-28 [1] CRAN (R 4.3.0)
## pbs 1.1 2013-06-08 [1] CRAN (R 4.3.0)
## pcaPP 2.0-3 2022-10-24 [1] CRAN (R 4.3.0)
## pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0)
## pkgbuild 1.4.2 2023-06-26 [1] CRAN (R 4.3.0)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
## pkgload 1.3.3 2023-09-22 [1] CRAN (R 4.3.1)
## plogr 0.2.0 2018-03-25 [1] CRAN (R 4.3.0)
## plot3D 1.4 2021-05-22 [1] CRAN (R 4.3.0)
## plyr 1.8.9 2023-10-02 [1] CRAN (R 4.3.1)
## png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0)
## polyclip 1.10-6 2023-09-27 [1] CRAN (R 4.3.1)
## pracma 2.4.4 2023-11-10 [1] CRAN (R 4.3.1)
## praise 1.0.0 2015-08-11 [1] CRAN (R 4.3.0)
## prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.3.1)
## processx 3.8.2 2023-06-30 [1] CRAN (R 4.3.0)
## progress 1.2.2 2019-05-16 [1] CRAN (R 4.3.0)
## promises 1.2.1 2023-08-10 [1] CRAN (R 4.3.0)
## ps 1.7.5 2023-04-18 [1] CRAN (R 4.3.0)
## purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.0)
## R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.3.0)
## R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.3.0)
## R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.3.0)
## R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0)
## ragg 1.2.5 2023-01-12 [1] CRAN (R 4.3.0)
## rainbow 3.7 2022-10-09 [1] CRAN (R 4.3.0)
## rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.3.0)
## RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.3.0)
## Rcpp 1.0.11 2023-07-06 [1] CRAN (R 4.3.0)
## RcppEigen 0.3.3.9.4 2023-11-02 [1] CRAN (R 4.3.1)
## RCurl 1.98-1.13 2023-11-02 [1] CRAN (R 4.3.1)
## readr 2.1.4 2023-02-10 [1] CRAN (R 4.3.0)
## readxl 1.4.3 2023-07-06 [1] CRAN (R 4.3.0)
## refund 0.1-33 2023-11-14 [1] CRAN (R 4.3.1)
## rematch 2.0.0 2023-08-30 [1] CRAN (R 4.3.0)
## rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.3.0)
## reprex 2.0.2 2022-08-17 [1] CRAN (R 4.3.0)
## reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.3.0)
## rhdf5 2.44.0 2023-05-08 [1] Bioconductor
## rhdf5filters 1.12.1 2023-05-08 [1] Bioconductor
## Rhdf5lib 1.22.1 2023-09-10 [1] Bioconductor
## rjson 0.2.21 2022-01-09 [1] CRAN (R 4.3.0)
## rlang 1.1.2 2023-11-04 [1] CRAN (R 4.3.1)
## RLRsim 3.1-8 2022-03-16 [1] CRAN (R 4.3.0)
## rmarkdown 2.25 2023-09-18 [1] CRAN (R 4.3.1)
## rpart 4.1.19 2022-10-21 [1] CRAN (R 4.3.1)
## rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.3.1)
## RSQLite 2.3.1 2023-04-03 [1] CRAN (R 4.3.0)
## rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.0)
## rvest 1.0.3 2022-08-19 [1] CRAN (R 4.3.0)
## S4Arrays 1.0.6 2023-09-10 [1] Bioconductor
## S4Vectors 0.38.1 2023-05-08 [1] Bioconductor
## sass 0.4.7 2023-07-15 [1] CRAN (R 4.3.0)
## scales 1.3.0 2023-11-28 [1] CRAN (R 4.3.1)
## scuttle 1.9.4 2023-01-23 [1] Bioconductor
## selectr 0.4-2 2019-11-20 [1] CRAN (R 4.3.0)
## shiny 1.7.5 2023-08-12 [1] CRAN (R 4.3.0)
## SingleCellExperiment 1.22.0 2023-05-08 [1] Bioconductor
## sitmo 2.0.2 2021-10-13 [1] CRAN (R 4.3.0)
## snow 0.4-4 2021-10-27 [1] CRAN (R 4.3.0)
## sourcetools 0.1.7-1 2023-02-01 [1] CRAN (R 4.3.0)
## sp 2.0-0 2023-06-22 [1] CRAN (R 4.3.0)
## sparseMatrixStats 1.12.2 2023-07-02 [1] Bioconductor
## SpatialExperiment 1.10.0 2023-05-08 [1] Bioconductor
## spatialTIME 1.3.4-2 2023-12-19 [1] CRAN (R 4.3.1)
## spatstat 3.0-7 2023-10-30 [1] CRAN (R 4.3.1)
## spatstat.data 3.0-3 2023-10-24 [1] CRAN (R 4.3.1)
## spatstat.explore 3.2-5 2023-10-22 [1] CRAN (R 4.3.1)
## spatstat.geom 3.2-7 2023-10-20 [1] CRAN (R 4.3.1)
## spatstat.linnet 3.1-3 2023-10-28 [1] CRAN (R 4.3.1)
## spatstat.model 3.2-8 2023-10-23 [1] CRAN (R 4.3.1)
## spatstat.random 3.2-2 2023-11-29 [1] CRAN (R 4.3.1)
## spatstat.sparse 3.0-3 2023-10-24 [1] CRAN (R 4.3.1)
## spatstat.utils 3.0-4 2023-10-24 [1] CRAN (R 4.3.1)
## splancs 2.01-44 2023-08-21 [1] CRAN (R 4.3.0)
## stringi 1.8.2 2023-11-23 [1] CRAN (R 4.3.1)
## stringr 1.5.1 2023-11-14 [1] CRAN (R 4.3.1)
## SummarizedExperiment 1.30.2 2023-06-11 [1] Bioconductor
## sys 3.4.2 2023-05-23 [1] CRAN (R 4.3.0)
## systemfonts 1.0.4 2022-02-11 [1] CRAN (R 4.3.0)
## tensor 1.5 2012-05-05 [1] CRAN (R 4.3.0)
## testthat 3.2.1 2023-12-02 [1] CRAN (R 4.3.1)
## textshaping 0.3.6 2021-10-13 [1] CRAN (R 4.3.0)
## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0)
## tidyr 1.3.0 2023-01-24 [1] CRAN (R 4.3.0)
## tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0)
## tidyverse 2.0.0 2023-02-22 [1] CRAN (R 4.3.0)
## timechange 0.2.0 2023-01-11 [1] CRAN (R 4.3.0)
## tinytex 0.46 2023-08-09 [1] CRAN (R 4.3.0)
## tzdb 0.4.0 2023-05-12 [1] CRAN (R 4.3.0)
## utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.1)
## uuid 1.1-1 2023-08-17 [1] CRAN (R 4.3.0)
## vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.1)
## VectraPolarisData 1.4.0 2023-04-27 [1] Bioconductor
## viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.0)
## vroom 1.6.3 2023-04-28 [1] CRAN (R 4.3.0)
## waldo 0.5.2 2023-11-02 [1] CRAN (R 4.3.1)
## withr 2.5.2 2023-10-30 [1] CRAN (R 4.3.1)
## xfun 0.40 2023-08-09 [1] CRAN (R 4.3.0)
## xml2 1.3.5 2023-07-06 [1] CRAN (R 4.3.0)
## xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0)
## XVector 0.40.0 2023-05-08 [1] Bioconductor
## yaml 2.3.7 2023-01-23 [1] CRAN (R 4.3.0)
## zlibbioc 1.46.0 2023-05-08 [1] Bioconductor
##
## [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
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