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Guidelines_Spatial_Transcriptomics.html
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<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"/><title>Guidelines Spatial Transcriptomics </title><style>
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</style></head><body><article id="d0b182fe-25fb-4cf0-ac41-9ae50804e31f" class="page sans"><header><div class="page-header-icon undefined"><span class="icon">🤖</span></div><h1 class="page-title">Guidelines Spatial Transcriptomics </h1></header><div class="page-body"><p id="be03e8f7-3f29-4497-8453-e70c3a61fecb" class="">This is a guide to install basic tools for ST analysis using a conda environment for the sake of reproducibility. </p><nav id="62adc41e-fc8e-4510-b30e-a275dcf40360" class="block-color-gray table_of_contents"><div class="table_of_contents-item table_of_contents-indent-0"><a class="table_of_contents-link" href="#44cb333f-a158-4bba-9851-6fe18d978330">Commands to follow</a></div><div class="table_of_contents-item table_of_contents-indent-0"><a class="table_of_contents-link" href="#5d42454b-4617-4f1d-bfa6-0bc088205a8f">Cluster</a></div></nav><h1 id="44cb333f-a158-4bba-9851-6fe18d978330" class="">Commands to follow</h1><p id="aca6a82c-97c0-4c17-be0c-d05e4db7fdc3" class="">This HTML was created with Notion. In Notion, you can create <code>inline code snippets</code> with the shortcut <code>cmd/ctrl + e</code>.</p><pre id="ee08e787-da9d-4eb1-acb0-243989b24a66" class="code"><code>conda create -n spatial_r
conda activate spatial_r
conda install -c conda-forge r-base=4.0.1</code></pre><p id="f6ec50e6-256f-40e9-aa0a-dfd03a5703db" class=""><strong>Install SPATA2</strong></p><p id="3c9b3be3-4d2d-4263-a23c-e41228dec9ca" class="">The following package is a dependency for some of the BiocManager packages that will be installed in the future.</p><pre id="1d2b17f2-31a1-4674-9ceb-7fe5f8d66277" class="code"><code>conda install -c eumetsat fftw3
#conda install -c conda-forge imagemagick #necessary for the cluster
#conda install -c conda-forge pandoc #necessary for the cluster</code></pre><p id="b4389309-2838-448f-9b5d-c5e0a5b4ee66" class="">Now let's go to R</p><pre id="3a13ca82-b0b7-4b48-976c-3355b4f0fcd6" class="code"><code>R</code></pre><pre id="5a2f28f5-732b-46cc-a26a-9de428db6a5d" class="code"><code>install.packages("devtools")
if (!base::requireNamespace("BiocManager", quietly = TRUE)){
install.packages("BiocManager")
}
BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',
'limma', 'S4Vectors', 'SingleCellExperiment',
'SummarizedExperiment', 'batchelor', 'Matrix.utils',
'EBImage'))
install.packages("Seurat")
devtools::install_github(repo = "kueckelj/confuns")</code></pre><p id="26377858-64dd-4606-8e1e-40de0de905f3" class="">Go back to the terminal and use conda to install the following:</p><pre id="d7a8ef00-5db0-46a8-ae50-6a6c47b0a044" class="code"><code>conda install -c conda-forge udunits2
##libgal package downstream will install proj and r-proj4 automatically
##but I pre-installed in this order of commands
#conda install -c conda-forge r-proj4
conda install -c conda-forge r-v8</code></pre><pre id="78118f7c-a709-405e-a987-62e7db803193" class="code"><code>##the commented lines were executed but I'm not sure those made any difference
#sudo apt remove libudunits2-dev libgdal-dev libgeos-dev libproj-dev
#sudo apt install libudunits2-dev libgdal-dev libgeos-dev libproj-dev libfontconfig1-dev
conda install -c conda-forge libgdal
R</code></pre><pre id="7a47a27b-ac43-4d7b-bb18-fc8e70208c8a" class="code"><code>install.packages("sf")
devtools::install_github(repo = "theMILOlab/SPATA2")
devtools::install_github('cole-trapnell-lab/leidenbase')
devtools::install_github('cole-trapnell-lab/leidenbase')</code></pre><p id="c83d33e2-085f-4074-9a15-bee5aec7b3fe" class=""><strong>Install common packages</strong></p><pre id="113d4c31-5a5d-45f2-8aea-98e417725c19" class="code"><code>install.packages("tidyverse")
install.packages("gt")
install.packages("ggpubr")
install.packages("ggrepel")
install.packages("rmarkdown")
install.packages("knitr")
install.packages("DT")
install.packages("here")
if (!requireNamespace("remotes", quietly = TRUE)) {
install.packages("remotes")
}
remotes::install_github("mojaveazure/seurat-disk")
#install.packages("spdep") #necessary for the cluster
devtools::install_github(
"jbergenstrahle/STUtility"
)
remotes::install_github("saezlab/mistyR")
BiocManager::install("progeny")
BiocManager::install("dorothea")</code></pre><p id="3dc8896b-bce2-43a4-a991-3d2d81dce0d3" class=""><strong>Install SPOTlight</strong></p><p id="97d6cdf5-9716-42b1-941d-770d1a3361f4" class="">In the terminal, install this </p><pre id="db1d9470-bb3a-499b-b4d4-f35bb6f42eea" class="code"><code>conda install -c anaconda gmp</code></pre><pre id="647bccc8-85e1-4fd1-9bb3-04f361e47c77" class="code"><code>install.packages("gmp")
install.packages("arrangements")</code></pre><p id="68e3d48b-62b1-41bb-8901-7e89868cbf23" class="">I encountered lots of problems to install <code>imager</code> from CRAN due to X11 library. That's why the following commands are commented because I don't know whether they influenced in the final installation of <code>r-imager</code> by conda.</p><pre id="5237cca8-3a27-4d45-ab47-bc32c3ca4a9e" class="code"><code>#conda install -c conda-forge xorg-libx11
#conda install -c borismarin libx11
#sudo apt install xorg
#sudo apt install libx11-dev
conda install -c conda-forge r-imager</code></pre><pre id="4b3258d7-4e2b-4f33-b1d9-9fb8d3852687" class="code"><code>devtools::install_github("https://github.com/MarcElosua/SPOTlight")</code></pre><p id="dcd59f8b-6f96-426f-ab15-08232d5e64c7" class=""><strong>Install Harmony</strong></p><pre id="c3c26598-d41c-46c1-b882-8be2852ea402" class="code"><code>devtools::install_github("immunogenomics/harmony")</code></pre><p id="5fc0b74d-8fb1-43ab-b7fd-836aea1e4306" class=""><strong>Install MAGIC</strong></p><pre id="2463b0c5-019f-40f0-85fd-4d58f65c23c6" class="code"><code>conda install -c bioconda scprep
conda install matplotlib future tasklogger graphtools scipy pandas Deprecated pygsp pytz python-dateutil six threadpoolctl joblib decorator wrapt cycler kiwisolver pyparsing pillow
conda install -c anaconda zlib
R
install.packages("Rmagic")</code></pre><h1 id="5d42454b-4617-4f1d-bfa6-0bc088205a8f" class="">Cluster</h1><p id="4b2a2bc3-abf8-4160-8ae5-05228245a1b7" class="">Load all these modules to be able to install SPATA2 in the cluster</p><pre id="2fb1fda3-85b3-4fbb-949a-34dae4382ac1" class="code"><code>module load R/4.0.1 PROJ/7.0.1 GDAL/2.4.2 GEOS/3.4.2 UDUNITS/2.2.26
install.packages("sf", configure.args = c(sf = "--with-proj-include=/apps/PROJ/7.0.1/include"))</code></pre><p id="bc50090d-41af-4a50-9b74-8da8ced0bb27" class="">
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