TGCA数据挖掘1---R包安装
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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> options("repos" = c(CRAN="mirrors.tuna.tsinghua.edu/CRAN/"))
> if(!require("BiocManager")) install.packages("BiocManager",update = F,ask = F)
载⼊需要的程辑包：BiocManager
Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help
>
> options(BioC_mirror="mirrors.tuna.tsinghua.edu/bioconductor/")
>
> cran_packages <- c('tidyr',
+                    'tibble',
+                    'dplyr',
+                    'stringr',
+                    'ggplot2',
+                    'ggpubr',
+                    'factoextra',
+                    'FactoMineR',
+                    'pheatmap',
+                    "survival",
+                    "survminer",
+                    "patchwork",
+                    "ggstatsplot",
+                    "ggplotify",
+                    "cowplot",
+                    "glmnet",
+                    "ROCR",
+                    "caret",
+                    "randomForest",
+                    "survminer",
+                    "Hmisc",
+                    "e1071",
+                    "deconstructSigs",
+                    "timeROC"
+ )
> Biocductor_packages <- c("KEGG.db",
+                          "limma",
+                          "clusterProfiler",
+                          "db",
+                          "SummarizedExperiment",
+                          "DESeq2",
+                          "edgeR",
+                          "ggpubr",
+                          "rtracklayer",
+                          "genefilter",
+                          "maftools",
+                          "ComplexHeatmap",
+                          "GDCRNATools"
+ )
>
>
> for (pkg in cran_packages){
+  if (! require(ly=T) ) {
+    install.packages(pkg,ask = F,update = F)
+    require(ly=T)
+  }
+ }
载⼊需要的程辑包：tidyr
载⼊需要的程辑包：tibble
载⼊需要的程辑包：dplyr
载⼊程辑包：‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
载⼊需要的程辑包：stringr
载⼊需要的程辑包：ggplot2
Use suppressPackageStartupMessages() to eliminate package startup messages
载⼊需要的程辑包：ggpubr
载⼊需要的程辑包：factoextra
Welcome! Want to learn more? See two factoextra-related books at goo.gl/ve3WBa 载⼊需要的程辑包：FactoMineR
载⼊需要的程辑包：pheatmap
载⼊需要的程辑包：survival
载⼊需要的程辑包：survminer
载⼊需要的程辑包：patchwork
载⼊需要的程辑包：ggstatsplot
Registered S3 methods overwritten by 'lme4':
method                          from
cooks.Mod car
Mod        car
Mod        car
In case you would like cite this package, cite it as:
Patil, I. (2018). ggstatsplot: "ggplot2" Based Plots with Statistical Details. CRAN.
Retrieved from /web/packages/ggstatsplot/index.html
载⼊需要的程辑包：ggplotify
载⼊需要的程辑包：cowplot
载⼊程辑包：‘cowplot’
The following object is masked from ‘package:patchwork’:
align_plots
The following object is masked from ‘package:ggpubr’:
get_legend
载⼊需要的程辑包：glmnet
载⼊需要的程辑包：Matrix
载⼊程辑包：‘Matrix’
The following objects are masked from ‘package:tidyr’:
expand, pack, unpack
Loaded glmnet 4.1
载⼊需要的程辑包：ROCR
载⼊需要的程辑包：caret
载⼊需要的程辑包：lattice
载⼊程辑包：‘caret’
The following object is masked from ‘package:survival’:
cluster
cluster
载⼊需要的程辑包：randomForest
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
载⼊程辑包：‘randomForest’
The following object is masked from ‘package:ggplot2’:
margin
The following object is masked from ‘package:dplyr’:
combine
载⼊需要的程辑包：Hmisc
载⼊需要的程辑包：Formula
载⼊程辑包：‘Hmisc’
The following objects are masked from ‘package:dplyr’:
src, summarize
The following objects are masked from ‘package:base’:
format.pval, units
载⼊需要的程辑包：e1071
载⼊程辑包：‘e1071’
The following object is masked from ‘package:Hmisc’:
impute
载⼊需要的程辑包：deconstructSigs
载⼊需要的程辑包：timeROC
>
>
> # use BiocManager to install
> for (pkg in Biocductor_packages){
+  if (! require(ly=T) ) {
+    BiocManager::install(pkg,ask = F,update = F)
+    require(ly=T)
+  }
+ }
载⼊需要的程辑包：KEGG.db
载⼊需要的程辑包：AnnotationDbi
载⼊需要的程辑包：stats4
载⼊需要的程辑包：BiocGenerics
载⼊需要的程辑包：parallel
载⼊程辑包：‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply,    parSapplyLB
The following object is masked from ‘package:randomForest’:
combine
The following objects are masked from ‘package:dplyr’:
combine, intersect, setdiff, union
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname,
do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which.max, which.min
载⼊需要的程辑包：Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite
Bioconductor, see 'citation("Biobase")', and for packages
'citation("pkgname")'.
载⼊程辑包：‘Biobase’
The following object is masked from ‘package:Hmisc’:
contents
载⼊需要的程辑包：IRanges
载⼊需要的程辑包：S4Vectors
载⼊程辑包：‘S4Vectors’
The following object is masked from ‘package:Matrix’:
expand
The following objects are masked from ‘package:dplyr’:
first, rename
The following object is masked from ‘package:tidyr’:
expand
The following object is masked from ‘package:base’:
载⼊程辑包：‘IRanges’
The following objects are masked from ‘package:dplyr’:
collapse, desc, slice
The following object is masked from ‘package:grDevices’:
windows
载⼊程辑包：‘AnnotationDbi’
The following object is masked from ‘package:dplyr’:
select
KEGG.db contains mappings based on older data because the original resource was  removed from the the public domain before the most recent update was produced.  This package should now be considered deprecated and future versions of
Bioconductor may not have it available.  Users who want more current data are
encouraged to look at the KEGGREST or reactome.db packages
载⼊需要的程辑包：limma
载⼊程辑包：‘limma’
The following object is masked from ‘package:BiocGenerics’:
plotMA
载⼊需要的程辑包：clusterProfiler
clusterProfiler v3.18.0  For help: guangchuangyu.github.io/software/clusterProfiler
If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integra 载⼊程辑包：‘clusterProfiler’
The following object is masked from ‘package:AnnotationDbi’:
select
The following object is masked from ‘package:IRanges’:
slice
The following object is masked from ‘package:S4Vectors’:
rename
The following object is masked from ‘package:lattice’:
dotplot
The following object is masked from ‘package:stats’:
filter
载⼊需要的程辑包：db
载⼊需要的程辑包：SummarizedExperiment
载⼊需要的程辑包：MatrixGenerics
载⼊需要的程辑包：matrixStats
载⼊程辑包：‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
The following object is masked from ‘package:dplyr’:
count
载⼊程辑包：‘MatrixGenerics’
The following objects are masked from ‘package:matrixStats’:
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts,
colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs,
colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians,
colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks,
colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars,
colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse,
rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs,
rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2,
rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges,
rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds,
rowWeightedVars
eval是做什么的The following object is masked from ‘package:Biobase’:
rowMedians
载⼊需要的程辑包：GenomicRanges

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