Updates conda envs for 2023

labs/environment_R2023.yml

@@ -0,0 +1,100 @@
+## conda requirements for all packages needed to run the scanpy tutorials
+# install with:  mamba env create -f environment_scRNAseq2023.yml
+# then run: source activate scRNAseq2023
+name: scRNAseq2023
+
+channels:
+### MAIN CONDA CHANNELS ###
+ - conda-forge
+ - bioconda
+ - defaults
+### ADDITIONAL CONDA CHANNELS ###
+
+dependencies:
+### GENERAL LIBRARIES ###
+ - r-base=4.2.2
+ - rstudio-desktop=2022.07.02
+ - wget
+ - qt-main=5.15.4 #needed for rstudio
+# - compilers
+# - openssl=1.0.2o
+# - pandoc=2.16.2
+### R BIOCONDUCTOR PACKAGES ##
+ - bioconductor-scater #=1.22.0
+ - bioconductor-scran #=1.22.0
+ - bioconductor-singlecellexperiment
+ - bioconductor-slingshot
+ - bioconductor-tradeseq
+# - bioconductor-destiny
+ - bioconductor-rhdf5
+ - bioconductor-fgsea
+ - bioconductor-biomart
+ - bioconductor-org.hs.eg.db
+ - bioconductor-scdblfinder
+ - bioconductor-biocsingular
+ - bioconductor-singler
+ - bioconductor-batchelor
+ - bioconductor-scmap
+ - bioconductor-glmgampoi
+ - bioconductor-scrnaseq
+ - bioconductor-mast
+ - bioconductor-dropletutils
+ - bioconductor-scdblfinder 
+### R CRAN PACKAGES ###
+ - r-emdbook
+ - r-rgl
+ - r-plot3d
+ - r-fastica
+ - r-irlba
+ - r-pheatmap
+ - r-msigdbr
+ - r-rafalib
+ - r-enrichr
+ - r-clustree
+ - r-devtools
+ - r-biocmanager
+ - r-rcpphnsw
+ - r-dplyr
+ - r-igraph
+ - r-seurat
+ - r-umap
+ - r-grr
+ - r-hdf5r
+ - r-bookdown
+ - r-venn
+ - r-uwot
+ - r-optparse
+ - r-fields
+ - r-ggraph
+ - r-checkmate
+ - r-tidygraph
+ - r-spam
+ - r-stringi
+ - r-stringr
+ - r-pkgmaker
+ - r-l1pack
+ - r-nnls
+ - r-reshape
+ - r-jpeg
+ - r-clustree
+ - r-mlmetrics
+ - r-caret
+ - r-kernlab
+ - r-proc
+ - r-msigdbr
+ - xbioc
+
+### PYTHON LIBRARIES ###
+ - multicore-tsne
+ - umap-learn
+
+# Manual installation of packages that are not in conda:
+# remotes::install_github('chris-mcginnis-ucsf/DoubletFinder', dependencies=FALSE)
+# remotes::install_github('satijalab/seurat-data', dependencies=FALSE)
+# remotes::install_github("meichendong/SCDC", dependencies = FALSE)
+
+
+# harmony not avail for R4.2.2, instead install from cran.
+#install.packages("harmony", dependencies=F)
+#devtools::install_github("powellgenomicslab/scPred",  dependencies=F)
+

labs/environment_python2023.yml

@@ -0,0 +1,22 @@
+name: scRNAseq2023_python
+channels:
+ - pytorch
+ - conda-forge
+ - bioconda
+ - defaults
+ - anaconda
+dependencies:
+ - python
+ - compilers
+ - pip
+ - scanpy
+ - jupyterlab
+ - scanorama
+ - nb_conda
+ - scvi-tools
+ - fa2   
+ - python-igraph
+ - pynndescent
+ - leidenalg
+ - louvain
+ - mkl < 2022 # needed for running intel conda on M1 mac.

labs/scater/scater_01_qc.Rmd

@@ -30,7 +30,10 @@ suppressMessages(require(scater))
 suppressMessages(require(scran))
 suppressMessages(require(cowplot))
 suppressMessages(require(org.Hs.eg.db))
-remotes::install_github('chris-mcginnis-ucsf/DoubletFinder',upgrade = F)
+
+if(!require(DoubletFinder){
+   remotes::install_github('chris-mcginnis-ucsf/DoubletFinder',upgrade = F, dependencies=F)
+}
 suppressMessages(require(DoubletFinder))
 ```
 
@@ -379,7 +382,6 @@ sce.filt <- runUMAP(sce.filt, pca = 10)
 ```
 
 ```{r}
-BiocManager::install('scDblFinder',update = F)
 suppressPackageStartupMessages(require(scDblFinder))
 
 # run computeDoubletDensity with 10 principal components.

labs/scater/scater_04_clustering.Rmd

@@ -13,7 +13,6 @@ editor_options:
 #CLUST_ALL2:
 
 ```{r, message='hide',warning='hide',results='hold'}
-if(!require(clustree)){install.packages('clustree', dependencies=FALSE)}
 
 suppressPackageStartupMessages({
   library(scater)
@@ -94,7 +93,6 @@ plot_grid(ncol = 3,
 
 
 ```{r}
-# install.packages("clustree")
 suppressPackageStartupMessages(library(clustree))
 
 clustree(sce, prefix = "louvain_SNNk")

labs/scater/scater_05_dge.Rmd

@@ -173,7 +173,6 @@ gene_rank <- setNames( DGE_cell_selection$Covid[,grep("logFC.C",colnames(DGE_cel
 #DGE_ALL7.3:
 
 ```{r,fig.height=10,fig.width=10}
-# install.packages("msigdbr")
 library(msigdbr)
 
 #Download gene sets

labs/seurat/seurat_01_qc.Rmd

@@ -29,7 +29,9 @@ for(i in file_list){
 ```{r, message='hide',warning='hide',results='hold'}
 suppressMessages(require(Seurat))
 suppressMessages(require(Matrix))
-remotes::install_github('chris-mcginnis-ucsf/DoubletFinder',upgrade = F)
+if(!require(DoubletFinder){
+   remotes::install_github('chris-mcginnis-ucsf/DoubletFinder',upgrade = FALSE, dependencies=FALSE)
+}
 suppressMessages(require(DoubletFinder))
 ```
 

labs/seurat/seurat_04_clustering.Rmd

@@ -13,7 +13,6 @@ editor_options:
 #CLUST_ALL2:
 
 ```{r, message='hide',warning='hide',results='hold'}
-if(!require(clustree)){install.packages('clustree', dependencies=FALSE)}
 
 suppressPackageStartupMessages({
   library(Seurat)
@@ -87,7 +86,6 @@ plot_grid(ncol = 3,
 
 
 ```{r}
-# install.packages("clustree")
 suppressPackageStartupMessages(library(clustree))
 
 clustree([email protected], prefix = "CCA_snn_res.")

labs/seurat/seurat_07_spatial.Rmd

@@ -14,7 +14,7 @@ This tutorial is adapted from the Seurat vignette: https://satijalab.org/seurat/
 #ST_TITLE1:
 
 ```{r packages}
-devtools::install_github('satijalab/seurat-data')
+devtools::install_github('satijalab/seurat-data', dependencies=FALSE)
 
 suppressPackageStartupMessages(require(Matrix))
 suppressPackageStartupMessages(require(dplyr))