From b5850bbfab0b63de2fb12d2b57c778ec9dbda5ce Mon Sep 17 00:00:00 2001 From: Shaojun Xie Date: Sun, 1 Dec 2024 23:32:47 -0500 Subject: [PATCH] Add docs/bioi611_prep_monocle_env.ipynb --- docs/bioi611_prep_monocle_env.ipynb | 382 ++++++++++++++++++++++++++++ 1 file changed, 382 insertions(+) create mode 100644 docs/bioi611_prep_monocle_env.ipynb 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" + ] + }, + { + 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"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