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Add docs/bioi611_prep_monocle_env.ipynb
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xie186 committed Dec 2, 2024
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"'getOption(\"repos\")' replaces Bioconductor standard repositories, see\n",
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"Replacement repositories:\n",
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" 'batchelor', 'HDF5Array', 'terra', 'ggrastr'\n",
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"Installing package into ‘/usr/local/lib/R/site-library’\n",
"(as ‘lib’ is unspecified)\n",
"\n",
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"plotly (NA -> 4.10.4 ) [CRAN]\n",
"pheatmap (NA -> 1.0.12 ) [CRAN]\n",
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"pbapply (NA -> 1.7-2 ) [CRAN]\n",
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"leidenbase (NA -> 0.1.31 ) [CRAN]\n",
"grr (NA -> 0.9.5 ) [CRAN]\n",
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"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"
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}
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},
{
"cell_type": "code",
"source": [
"library(monocle3)"
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{
"output_type": "stream",
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"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",
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" colWeightedMeans, colWeightedMedians, colWeightedSds,\n",
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" 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"
]
}
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{
"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": []
}
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}

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