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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>About This Website</title>
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<body>
<div class="container-fluid main-container">
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">Analysis of multiplex single-cell imaging data in R</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">Home</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Short Course
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="MI_Data.html">Data Download</a>
</li>
<li>
<a href="MI_intro.html">Background on multiplex single-cell imaging</a>
</li>
<li>
<a href="MI_VectraPolarisData.html">VectraPolarisData package</a>
</li>
<li>
<a href="MI_normalization.html">Segmentation, normalization, and phenotyping</a>
</li>
<li>
<a href="MI_spatialAnalysis.html">Extracting spatial summary statistics</a>
</li>
<li>
<a href="MI_fda.html">Modeling patient-level outcomes</a>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="about.html">About</a>
</li>
<li>
<a href="https://github.com/julia-wrobel/MI_tutorial">
<span class="fa fa-github fa-lg"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div id="header">
<h1 class="title toc-ignore">About This Website</h1>
</div>
<p>This is an <a
href="http://rmarkdown.rstudio.com/rmarkdown_websites.html">R Markdown
website</a>, created by <a href="http://juliawrobel.com">Julia
Wrobel</a> for a multiplex single-cell imaging data workshop at the
University of Michigan Department of Biostatistics.</p>
<p>In the short course, we’ll actively 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.</p>
<p>Installing packages from CRAN</p>
<pre class="r"><code># main packages
install.packages(c("tidyverse", "spatstat", "spatialTIME", "mxnorm","refund",
"refund.shiny", "tiff", "survival"))
# additional packages used for visualization
install.packages(c("viridis", "patchwork"))</code></pre>
<p>Installing packages from Bioconductor</p>
<pre class="r"><code># install Bioconductor
BiocManager::install(version = "3.16")
# VectraPolarisData
BiocManager::install("VectraPolarisData")
# EBImage
BiocManager::install("EBImage")</code></pre>
<p>Versions of key packages:</p>
<pre class="r"><code>devtools::session_info(c("tidyverse", "VectraPolarisData", "spatstat", "spatialTIME", "refund"))</code></pre>
<pre><code>## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.2.3 (2023-03-15)
## os macOS Big Sur ... 10.16
## system x86_64, darwin17.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/Denver
## date 2023-04-04
## pandoc 2.19.2 @ /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 4.2.0)
## AnnotationDbi 1.60.2 2023-03-10 [1] Bioconductor
## AnnotationHub 3.6.0 2022-11-01 [1] Bioconductor
## ash 1.0-15 2015-09-01 [1] CRAN (R 4.2.0)
## askpass 1.1 2019-01-13 [1] CRAN (R 4.2.0)
## backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0)
## base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.2.0)
## beachmat 2.14.0 2022-11-01 [1] Bioconductor
## BH 1.81.0-1 2023-01-22 [1] CRAN (R 4.2.0)
## Biobase 2.58.0 2022-11-01 [1] Bioconductor
## BiocFileCache 2.6.1 2023-02-17 [1] Bioconductor
## BiocGenerics 0.44.0 2022-11-01 [1] Bioconductor
## BiocManager 1.30.20 2023-02-24 [1] CRAN (R 4.2.0)
## BiocParallel 1.32.6 2023-03-17 [1] Bioconductor
## BiocVersion 3.16.0 2022-05-05 [1] Bioconductor
## Biostrings 2.66.0 2022-11-01 [1] Bioconductor
## bit 4.0.5 2022-11-15 [1] CRAN (R 4.2.0)
## bit64 4.0.5 2020-08-30 [1] CRAN (R 4.2.0)
## bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0)
## blob 1.2.4 2023-03-17 [1] CRAN (R 4.2.0)
## boot 1.3-28.1 2022-11-22 [1] CRAN (R 4.2.3)
## brio 1.1.3 2021-11-30 [1] CRAN (R 4.2.0)
## broom 1.0.4 2023-03-11 [1] CRAN (R 4.2.0)
## bslib 0.4.2 2022-12-16 [1] CRAN (R 4.2.0)
## cachem 1.0.7 2023-02-24 [1] CRAN (R 4.2.0)
## callr 3.7.3 2022-11-02 [1] CRAN (R 4.2.0)
## cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.2.0)
## cli 3.6.1 2023-03-23 [1] CRAN (R 4.2.0)
## clipr 0.8.0 2022-02-22 [1] CRAN (R 4.2.0)
## cluster 2.1.4 2022-08-22 [1] CRAN (R 4.2.3)
## codetools 0.2-19 2023-02-01 [1] CRAN (R 4.2.3)
## colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.2.0)
## commonmark 1.9.0 2023-03-17 [1] CRAN (R 4.2.0)
## conflicted 1.2.0 2023-02-01 [1] CRAN (R 4.2.0)
## cpp11 0.4.3 2022-10-12 [1] CRAN (R 4.2.0)
## crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0)
## crosstalk 1.2.0 2021-11-04 [1] CRAN (R 4.2.0)
## curl 5.0.0 2023-01-12 [1] CRAN (R 4.2.0)
## data.table 1.14.8 2023-02-17 [1] CRAN (R 4.2.0)
## DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0)
## dbplyr 2.3.2 2023-03-21 [1] CRAN (R 4.2.0)
## DelayedArray 0.24.0 2022-11-01 [1] Bioconductor
## DelayedMatrixStats 1.20.0 2022-11-01 [1] Bioconductor
## deldir 1.0-6 2021-10-23 [1] CRAN (R 4.2.0)
## desc 1.4.2 2022-09-08 [1] CRAN (R 4.2.0)
## deSolve 1.35 2023-03-12 [1] CRAN (R 4.2.0)
## diffobj 0.3.5 2021-10-05 [1] CRAN (R 4.2.0)
## digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.0)
## dplyr 1.1.1 2023-03-22 [1] CRAN (R 4.2.0)
## dqrng 0.3.0 2021-05-01 [1] CRAN (R 4.2.0)
## DropletUtils 1.18.1 2022-11-22 [1] Bioconductor
## DT 0.27 2023-01-17 [1] CRAN (R 4.2.0)
## dtplyr 1.3.1 2023-03-22 [1] CRAN (R 4.2.0)
## edgeR 3.40.2 2023-01-19 [1] Bioconductor
## ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
## evaluate 0.20 2023-01-17 [1] CRAN (R 4.2.0)
## ExperimentHub 2.6.0 2022-11-01 [1] Bioconductor
## fansi 1.0.4 2023-01-22 [1] CRAN (R 4.2.0)
## farver 2.1.1 2022-07-06 [1] CRAN (R 4.2.0)
## fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.2.0)
## fda 6.0.5 2022-07-04 [1] CRAN (R 4.2.0)
## fds 1.8 2018-10-31 [1] CRAN (R 4.2.0)
## filelock 1.0.2 2018-10-05 [1] CRAN (R 4.2.0)
## FNN 1.1.3.2 2023-03-20 [1] CRAN (R 4.2.0)
## fontawesome 0.5.0 2023-01-25 [1] CRAN (R 4.2.0)
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## formatR 1.14 2023-01-17 [1] CRAN (R 4.2.0)
## fs 1.6.1 2023-02-06 [1] CRAN (R 4.2.0)
## furrr 0.3.1 2022-08-15 [1] CRAN (R 4.2.0)
## futile.logger 1.4.3 2016-07-10 [1] CRAN (R 4.2.0)
## futile.options 1.0.1 2018-04-20 [1] CRAN (R 4.2.0)
## future 1.32.0 2023-03-07 [1] CRAN (R 4.2.0)
## gamm4 0.2-6 2020-04-03 [1] CRAN (R 4.2.0)
## gargle 1.3.0 2023-01-30 [1] CRAN (R 4.2.0)
## generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
## GenomeInfoDb 1.34.9 2023-02-02 [1] Bioconductor
## GenomeInfoDbData 1.2.9 2023-03-24 [1] Bioconductor
## GenomicRanges 1.50.2 2022-12-16 [1] Bioconductor
## ggplot2 3.4.1 2023-02-10 [1] CRAN (R 4.2.0)
## globals 0.16.2 2022-11-21 [1] CRAN (R 4.2.0)
## glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
## goftest 1.2-3 2021-10-07 [1] CRAN (R 4.2.0)
## googledrive 2.1.0 2023-03-22 [1] CRAN (R 4.2.0)
## googlesheets4 1.1.0 2023-03-23 [1] CRAN (R 4.2.0)
## grpreg 3.4.0 2021-07-26 [1] CRAN (R 4.2.0)
## gtable 0.3.3 2023-03-21 [1] CRAN (R 4.2.0)
## haven 2.5.2 2023-02-28 [1] CRAN (R 4.2.0)
## HDF5Array 1.26.0 2022-11-01 [1] Bioconductor
## hdrcde 3.4 2021-01-18 [1] CRAN (R 4.2.0)
## highr 0.10 2022-12-22 [1] CRAN (R 4.2.0)
## hms 1.1.3 2023-03-21 [1] CRAN (R 4.2.0)
## htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.2.0)
## htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.2.0)
## httpuv 1.6.9 2023-02-14 [1] CRAN (R 4.2.0)
## httr 1.4.5 2023-02-24 [1] CRAN (R 4.2.0)
## ids 1.0.1 2017-05-31 [1] CRAN (R 4.2.0)
## interactiveDisplayBase 1.36.0 2022-11-01 [1] Bioconductor
## IRanges 2.32.0 2022-11-01 [1] Bioconductor
## isoband 0.2.7 2022-12-20 [1] CRAN (R 4.2.0)
## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.2.0)
## jsonlite 1.8.4 2022-12-06 [1] CRAN (R 4.2.0)
## KEGGREST 1.38.0 2022-11-01 [1] Bioconductor
## kernlab 0.9-32 2023-01-31 [1] CRAN (R 4.2.0)
## KernSmooth 2.23-20 2021-05-03 [1] CRAN (R 4.2.3)
## knitr 1.42 2023-01-25 [1] CRAN (R 4.2.0)
## ks 1.14.0 2022-11-24 [1] CRAN (R 4.2.0)
## labeling 0.4.2 2020-10-20 [1] CRAN (R 4.2.0)
## lambda.r 1.2.4 2019-09-18 [1] CRAN (R 4.2.0)
## later 1.3.0 2021-08-18 [1] CRAN (R 4.2.0)
## lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.3)
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## limma 3.54.2 2023-02-28 [1] Bioconductor
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## lme4 1.1-32 2023-03-14 [1] CRAN (R 4.2.0)
## locfit 1.5-9.7 2023-01-02 [1] CRAN (R 4.2.0)
## lubridate 1.9.2 2023-02-10 [1] CRAN (R 4.2.0)
## magic 1.6-1 2022-11-16 [1] CRAN (R 4.2.0)
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## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
## MASS 7.3-58.3 2023-03-07 [1] CRAN (R 4.2.0)
## Matrix 1.5-3 2022-11-11 [1] CRAN (R 4.2.3)
## MatrixGenerics 1.10.0 2022-11-01 [1] Bioconductor
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## modelr 0.1.11 2023-03-22 [1] CRAN (R 4.2.0)
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## pbs 1.1 2013-06-08 [1] CRAN (R 4.2.0)
## pcaPP 2.0-3 2022-10-24 [1] CRAN (R 4.2.0)
## pillar 1.9.0 2023-03-22 [1] CRAN (R 4.2.0)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
## pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.2.0)
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## pracma 2.4.2 2022-09-22 [1] CRAN (R 4.2.0)
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## Rhdf5lib 1.20.0 2022-11-01 [1] Bioconductor
## rjson 0.2.21 2022-01-09 [1] CRAN (R 4.2.0)
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## RLRsim 3.1-8 2022-03-16 [1] CRAN (R 4.2.0)
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## selectr 0.4-2 2019-11-20 [1] CRAN (R 4.2.0)
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## SingleCellExperiment 1.20.1 2023-03-17 [1] Bioconductor
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## snow 0.4-4 2021-10-27 [1] CRAN (R 4.2.0)
## sourcetools 0.1.7-1 2023-02-01 [1] CRAN (R 4.2.0)
## sparseMatrixStats 1.10.0 2022-11-01 [1] Bioconductor
## SpatialExperiment 1.8.1 2023-03-05 [1] Bioconductor
## spatialTIME 1.3.3-3 2023-03-22 [1] CRAN (R 4.2.0)
## spatstat 3.0-3 2023-01-28 [1] CRAN (R 4.2.0)
## spatstat.data 3.0-1 2023-03-12 [1] CRAN (R 4.2.0)
## spatstat.explore 3.1-0 2023-03-14 [1] CRAN (R 4.2.0)
## spatstat.geom 3.1-0 2023-03-12 [1] CRAN (R 4.2.0)
## spatstat.linnet 3.0-6 2023-02-22 [1] CRAN (R 4.2.0)
## spatstat.model 3.2-1 2023-02-15 [1] CRAN (R 4.2.0)
## spatstat.random 3.1-4 2023-03-13 [1] CRAN (R 4.2.0)
## spatstat.sparse 3.0-1 2023-03-12 [1] CRAN (R 4.2.0)
## spatstat.utils 3.0-2 2023-03-11 [1] CRAN (R 4.2.0)
## stringi 1.7.12 2023-01-11 [1] CRAN (R 4.2.0)
## stringr 1.5.0 2022-12-02 [1] CRAN (R 4.2.0)
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## textshaping 0.3.6 2021-10-13 [1] CRAN (R 4.2.0)
## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.2.0)
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## utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.0)
## uuid 1.1-0 2022-04-19 [1] CRAN (R 4.2.0)
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## VectraPolarisData 1.2.0 2022-11-03 [1] Bioconductor
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## vroom 1.6.1 2023-01-22 [1] CRAN (R 4.2.0)
## waldo 0.4.0 2022-03-16 [1] CRAN (R 4.2.0)
## withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
## xfun 0.38 2023-03-24 [1] CRAN (R 4.2.3)
## xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.0)
## xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0)
## XVector 0.38.0 2022-11-01 [1] Bioconductor
## yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.0)
## zlibbioc 1.44.0 2022-11-01 [1] Bioconductor
##
## [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
##
## ──────────────────────────────────────────────────────────────────────────────</code></pre>
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