diff --git a/docs/bioi611_prep_monocle_env.ipynb b/docs/bioi611_prep_monocle_env.ipynb new file mode 100644 index 0000000..eb4a824 --- /dev/null +++ b/docs/bioi611_prep_monocle_env.ipynb @@ -0,0 +1,382 @@ +{ + "nbformat": 4, + "nbformat_minor": 0, + "metadata": { + "colab": { + "provenance": [], + "authorship_tag": "ABX9TyOo+y0ql/jI6JYUKYoqugZ5", + "include_colab_link": true + }, + "kernelspec": { + "name": "ir", + "display_name": "R" + }, + "language_info": { + "name": "R" + } + }, + "cells": [ + { + "cell_type": "markdown", + "metadata": { + "id": "view-in-github", + "colab_type": "text" + }, + "source": [ + "\"Open" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "AZHa-1NhvDW3", + "outputId": "6916a0e1-4f33-461c-f0b3-36b7a6017318" + }, + "outputs": [ + { + "output_type": "stream", + "name": "stderr", + "text": [ + "Installing package into ‘/usr/local/lib/R/site-library’\n", + "(as ‘lib’ is unspecified)\n", + "\n", + "'getOption(\"repos\")' replaces Bioconductor standard repositories, see\n", + "'help(\"repositories\", package = \"BiocManager\")' for details.\n", + "Replacement repositories:\n", + " CRAN: https://cran.rstudio.com\n", + "\n", + "Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.2 (2024-10-31)\n", + "\n", + "Installing package(s) 'BiocVersion'\n", + "\n" + ] + } + ], + "source": [ + "if (!requireNamespace(\"BiocManager\", quietly = TRUE))\n", + "install.packages(\"BiocManager\")\n", + "BiocManager::install(version = \"3.20\")" + ] + }, + { + "cell_type": "code", + "source": [ + "## required by scater package\n", + "system(\"apt-get install libx11-dev libcairo2-dev\") #, intern = TRUE)" + ], + "metadata": { + "id": "aADYiY5rzTif" + }, + "execution_count": null, + "outputs": [] + }, + { + "cell_type": "code", + "source": [ + "BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',\n", + " 'limma', 'lme4', 'S4Vectors', 'SingleCellExperiment',\n", + " 'SummarizedExperiment', 'batchelor', 'HDF5Array',\n", + " 'terra', 'ggrastr'))" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "_ff61jVEvcgt", + "outputId": "71657c73-38a4-431f-bd14-fd7991ca1109" + }, + "execution_count": null, + "outputs": [ + { + "output_type": "stream", + "name": "stderr", + "text": [ + "'getOption(\"repos\")' replaces Bioconductor standard repositories, see\n", + "'help(\"repositories\", package = \"BiocManager\")' for details.\n", + "Replacement repositories:\n", + " CRAN: https://cran.rstudio.com\n", + "\n", + "Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.2 (2024-10-31)\n", + "\n", + "Installing package(s) 'BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',\n", + " 'limma', 'lme4', 'S4Vectors', 'SingleCellExperiment', 'SummarizedExperiment',\n", + " 'batchelor', 'HDF5Array', 'terra', 'ggrastr'\n", + "\n", + "also installing the dependencies ‘formatR’, ‘zlibbioc’, ‘lambda.r’, ‘futile.options’, ‘matrixStats’, ‘abind’, ‘XVector’, ‘UCSC.utils’, ‘GenomeInfoDbData’, ‘assorthead’, ‘irlba’, ‘rsvd’, ‘futile.logger’, ‘snow’, ‘BH’, ‘beeswarm’, ‘vipor’, ‘MatrixGenerics’, ‘IRanges’, ‘S4Arrays’, ‘SparseArray’, ‘sparseMatrixStats’, ‘statmod’, ‘minqa’, ‘nloptr’, ‘RcppEigen’, ‘GenomicRanges’, ‘Biobase’, ‘GenomeInfoDb’, ‘igraph’, ‘BiocNeighbors’, ‘BiocSingular’, ‘BiocParallel’, ‘scuttle’, ‘ResidualMatrix’, ‘ScaledMatrix’, ‘beachmat’, ‘rhdf5’, ‘rhdf5filters’, ‘Rhdf5lib’, ‘Cairo’, ‘ggbeeswarm’, ‘png’\n", + "\n", + "\n" + ] + } + ] + }, + { + "cell_type": "code", + "source": [ + "install.packages(\"devtools\")\n", + "devtools::install_github('cole-trapnell-lab/monocle3')" + ], + "metadata": { + "id": "IsOXpzfjvjRs", + "colab": { + "base_uri": "https://localhost:8080/" + }, + "outputId": "69a809b5-baa4-40ea-8234-a305b60ce159" + }, + "execution_count": null, + "outputs": [ + { + "output_type": "stream", + "name": "stderr", + "text": [ + "Installing package into ‘/usr/local/lib/R/site-library’\n", + "(as ‘lib’ is unspecified)\n", + "\n", + "Downloading GitHub repo cole-trapnell-lab/monocle3@HEAD\n", + "\n" + ] + }, + { + "output_type": "stream", + "name": "stdout", + "text": [ + "sitmo (NA -> 2.0.2 ) [CRAN]\n", + "bitops (NA -> 1.0-9 ) [CRAN]\n", + "RCurl (NA -> 1.98-1.16) [CRAN]\n", + "proxy (NA -> 0.4-27 ) [CRAN]\n", + "wk (NA -> 0.9.4 ) [CRAN]\n", + "e1071 (NA -> 1.7-16 ) [CRAN]\n", + "units (NA -> 0.8-5 ) [CRAN]\n", + "s2 (NA -> 1.1.7 ) [CRAN]\n", + "classInt (NA -> 0.4-10 ) [CRAN]\n", + "sp (NA -> 2.1-4 ) [CRAN]\n", + "warp (NA -> 0.2.1 ) [CRAN]\n", + "parallelly (NA -> 1.39.0 ) [CRAN]\n", + "listenv (NA -> 0.9.1 ) [CRAN]\n", + "globals (NA -> 0.16.3 ) [CRAN]\n", + "future (NA -> 1.34.0 ) [CRAN]\n", + "lazyeval (NA -> 0.2.2 ) [CRAN]\n", + "RcppHNSW (NA -> 0.6.0 ) [CRAN]\n", + "gridExtra (NA -> 2.3 ) [CRAN]\n", + "RcppProgress (NA -> 0.4.2 ) [CRAN]\n", + "dqrng (NA -> 0.4.1 ) [CRAN]\n", + "RSpectra (NA -> 0.16-2 ) [CRAN]\n", + "RcppAnnoy 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[CRAN]\n", + "grr (NA -> 0.9.5 ) [CRAN]\n", + "ggrepel (NA -> 0.9.6 ) [CRAN]\n", + "assertthat (NA -> 0.2.1 ) [CRAN]\n" + ] + }, + { + "output_type": "stream", + "name": "stderr", + "text": [ + "Skipping 30 packages ahead of CRAN: zlibbioc, XVector, SparseArray, S4Arrays, IRanges, S4Vectors, MatrixGenerics, BiocGenerics, GenomeInfoDbData, GenomeInfoDb, Rhdf5lib, rhdf5filters, DelayedArray, Biobase, sparseMatrixStats, beachmat, DelayedMatrixStats, SummarizedExperiment, GenomicRanges, BiocParallel, SingleCellExperiment, ScaledMatrix, rhdf5, ResidualMatrix, scuttle, BiocSingular, BiocNeighbors, limma, HDF5Array, batchelor\n", + "\n", + "Installing 52 packages: sitmo, bitops, RCurl, proxy, wk, e1071, units, s2, classInt, sp, warp, parallelly, listenv, globals, future, lazyeval, RcppHNSW, gridExtra, RcppProgress, dqrng, RSpectra, RcppAnnoy, FNN, biglm, deldir, sf, spData, slider, furrr, plyr, crosstalk, zoo, viridis, uwot, speedglm, spdep, slam, Rtsne, RhpcBLASctl, rsample, reshape2, RANN, pscl, plotly, pheatmap, pbmcapply, pbapply, lmtest, leidenbase, grr, ggrepel, assertthat\n", + "\n", + "Installing packages into ‘/usr/local/lib/R/site-library’\n", + "(as ‘lib’ is unspecified)\n", + "\n" + ] + }, + { + "output_type": "stream", + "name": "stdout", + "text": [ + "\u001b[36m──\u001b[39m \u001b[36mR CMD build\u001b[39m \u001b[36m─────────────────────────────────────────────────────────────────\u001b[39m\n", + "* checking for file ‘/tmp/RtmpNviskA/remotesfa163c8a18/cole-trapnell-lab-monocle3-98402ed/DESCRIPTION’ ... OK\n", + "* preparing ‘monocle3’:\n", + "* checking DESCRIPTION meta-information ... OK\n", + "* cleaning src\n", + "* checking for LF line-endings in source and make files and shell scripts\n", + "* checking for empty or unneeded directories\n", + "Omitted ‘LazyData’ from DESCRIPTION\n", + "* building ‘monocle3_1.3.7.tar.gz’\n", + "\n" + ] + }, + { + "output_type": "stream", + "name": "stderr", + "text": [ + "Installing package into ‘/usr/local/lib/R/site-library’\n", + "(as ‘lib’ is unspecified)\n", + "\n" + ] + } + ] + }, + { + "cell_type": "code", + "source": [ + "library(monocle3)" + ], + "metadata": { + "id": "QJ84ioTIvpSW", + "colab": { + "base_uri": "https://localhost:8080/" + }, + "outputId": "57513973-4834-4688-ee82-9a0f7f8161a7" + }, + "execution_count": null, + "outputs": [ + { + "output_type": "stream", + "name": "stderr", + "text": [ + "Loading required package: Biobase\n", + "\n", + "Loading required package: BiocGenerics\n", + "\n", + "\n", + "Attaching package: ‘BiocGenerics’\n", + "\n", + "\n", + "The following objects are masked from ‘package:stats’:\n", + "\n", + " IQR, mad, sd, var, xtabs\n", + "\n", + "\n", + "The following objects are masked from ‘package:base’:\n", + "\n", + " anyDuplicated, aperm, append, as.data.frame, basename, cbind,\n", + " colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,\n", + " get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,\n", + " match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,\n", + " Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,\n", + " table, tapply, union, unique, unsplit, which.max, which.min\n", + "\n", + "\n", + "Welcome to Bioconductor\n", + "\n", + " Vignettes contain introductory material; view with\n", + " 'browseVignettes()'. To cite Bioconductor, see\n", + " 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n", + "\n", + "\n", + "Loading required package: SingleCellExperiment\n", + "\n", + "Loading required package: SummarizedExperiment\n", + "\n", + "Loading required package: MatrixGenerics\n", + "\n", + "Loading required package: matrixStats\n", + "\n", + "\n", + "Attaching package: ‘matrixStats’\n", + "\n", + "\n", + "The following objects are masked from ‘package:Biobase’:\n", + "\n", + " anyMissing, rowMedians\n", + "\n", + "\n", + "\n", + "Attaching package: ‘MatrixGenerics’\n", + "\n", + "\n", + "The following objects are masked from ‘package:matrixStats’:\n", + "\n", + " colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,\n", + " colCounts, colCummaxs, colCummins, colCumprods, colCumsums,\n", + " colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,\n", + " colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,\n", + " colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,\n", + " colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,\n", + " colWeightedMeans, colWeightedMedians, colWeightedSds,\n", + " colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,\n", + " rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,\n", + " rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,\n", + " rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,\n", + " rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,\n", + " rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,\n", + " rowWeightedMads, rowWeightedMeans, rowWeightedMedians,\n", + " rowWeightedSds, rowWeightedVars\n", + "\n", + "\n", + "The following object is masked from ‘package:Biobase’:\n", + "\n", + " rowMedians\n", + "\n", + "\n", + "Loading required package: GenomicRanges\n", + "\n", + "Loading required package: stats4\n", + "\n", + "Loading required package: S4Vectors\n", + "\n", + "\n", + "Attaching package: ‘S4Vectors’\n", + "\n", + "\n", + "The following object is masked from ‘package:utils’:\n", + "\n", + " findMatches\n", + "\n", + "\n", + "The following objects are masked from ‘package:base’:\n", + "\n", + " expand.grid, I, unname\n", + "\n", + "\n", + "Loading required package: IRanges\n", + "\n", + "Loading required package: GenomeInfoDb\n", + "\n", + "\n", + "Attaching package: ‘monocle3’\n", + "\n", + "\n", + "The following objects are masked from ‘package:Biobase’:\n", + "\n", + " exprs, fData, fData<-, pData, pData<-\n", + "\n", + "\n" + ] + } + ] + }, + { + "cell_type": "code", + "source": [ + "system(\"tar zcvf R_lib_monocle3.tar.gz /usr/local/lib/R/site-library\")" + ], + "metadata": { + "id": "HcNuTF5tC3-o" + }, + "execution_count": null, + "outputs": [] + } + ] +} \ No newline at end of file