This repository was designed to save the pipeline and scripts of analysis of 16 SrRNA gene datasets.
R version 3.6.0 (2019-04-26) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C
[3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8
[7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached): [1] compiler_3.6.0
.packages(all.available=T) [1] "dynamicTreeCut" "fastcluster" "foreach"
[4] "iterators" "abind" "acepack"
[7] "ade4" "animation" "AnnotationDbi"
[10] "ape" "askpass" "assertthat"
[13] "backports" "base" "base64enc"
[16] "bayesm" "BH" "Biobase"
[19] "BiocFileCache" "BiocGenerics" "BiocManager"
[22] "BiocVersion" "biom" "biomaRt"
[25] "bit" "bit64" "bitops"
[28] "blob" "boot" "brew"
[31] "broom" "Cairo" "callr"
[34] "car" "carData" "caTools"
[37] "cellranger" "checkmate" "class"
[40] "cli" "clipr" "clisymbols"
[43] "cluster" "clusterGeneration" "clusterSim"
[46] "coda" "codetools" "colorspace"
[49] "combinat" "commonmark" "compiler"
[52] "compositions" "corrplot" "covr"
[55] "cowplot" "crayon" "crosstalk"
[58] "curl" "data.table" "datasets"
[61] "DBI" "dbplyr" "dendextend"
[64] "DEoptimR" "desc" "devtools"
[67] "digest" "dlstats" "doParallel"
[70] "dplyr" "DT" "e1071"
[73] "ellipse" "ellipsis" "evaluate"
[76] "exactRankTests" "expm" "factoextra"
[79] "FactoMineR" "fansi" "farver"
[82] "fastmap" "fastmatch" "flashClust"
[85] "forcats" "forecast" "foreign"
[88] "formatR" "formattable" "Formula"
[91] "fracdiff" "fs" "furrr"
[94] "futile.logger" "futile.options" "future"
[97] "gdata" "generics" "getopt"
[100] "gganimate" "ggforce" "ggimage"
[103] "gglayer" "ggplot2" "ggplotify"
[106] "ggpubr" "ggraph" "ggrepel"
[109] "ggsci" "ggsignif" "ggtern"
[112] "ggtree" "gh" "git2r"
[115] "githubinstall" "globals" "glue"
[118] "GO.db" "gplots" "graphics"
[121] "graphlayouts" "grDevices" "greybox"
[124] "grid" "gridExtra" "gridGraphics"
[127] "gtable" "gtools" "GUniFrac"
[130] "haven" "hexbin" "highr"
[133] "Hmisc" "hms" "htmlTable"
[136] "htmltools" "htmlwidgets" "httpuv"
[139] "httr" "igraph" "impute"
[142] "ini" "IRanges" "jpeg"
[145] "jsonlite" "KernSmooth" "knitr"
[148] "labeling" "lambda.r" "lamW"
[151] "later" "latex2exp" "lattice"
[154] "latticeExtra" "lavaan" "lazyeval"
[157] "leaps" "lifecycle" "listenv"
[160] "lme4" "lmtest" "lubridate"
[163] "magick" "magrittr" "manipulateWidget"
[166] "maps" "maptools" "markdown"
[169] "MASS" "Matrix" "MatrixModels"
[172] "matrixStats" "meme" "memoise"
[175] "methods" "mgcv" "microbiomeViz"
[178] "mime" "miniUI" "minqa"
[181] "mnormt" "mockery" "modelr"
[184] "munsell" "nlme" "nloptr"
[187] "nnet" "numDeriv" "openssl"
[190] "openxlsx" "optparse" "parallel"
[193] "patchwork" "pbivnorm" "pbkrtest"
[196] "PerformanceAnalytics" "permute" "phangorn"
[199] "pheatmap" "phytools" "picante"
[202] "pillar" "pkgbuild" "pkgconfig"
[205] "pkgload" "plogr" "plotly"
[208] "plotrix" "plyr" "png"
[211] "polyclip" "polynom" "pracma"
[214] "praise" "preprocessCore" "prettyunits"
[217] "pROC" "processx" "progress"
[220] "promises" "proto" "ps"
[223] "psych" "purrr" "qiimer"
[226] "qrcode" "quadprog" "quantmod"
[229] "quantreg" "R.cache" "R.methodsS3"
[232] "R.oo" "R.utils" "R2HTML"
[235] "R6" "randomForest" "rappdirs"
[238] "rcmdcheck" "RColorBrewer" "Rcpp"
[241] "RcppArmadillo" "RcppEigen" "RcppParallel"
[244] "readr" "readxl" "rematch"
[247] "remotes" "reprex" "reshape2"
[250] "rex" "rgl" "rio"
[253] "RISmed" "rJava" "RJSONIO"
[256] "rlang" "rmarkdown" "robustbase"
[259] "roxygen2" "rpart" "rprojroot"
[262] "RSQLite" "rstudioapi" "rsvg"
[265] "rvcheck" "rversions" "rvest"
[268] "S4Vectors" "scales" "scatterplot3d"
[271] "scholar" "selectr" "sessioninfo"
[274] "shiny" "showtext" "showtextdb"
[277] "smooth" "sourcetools" "sp"
[280] "SparseM" "spatial" "splines"
[283] "statmod" "stats" "stats4"
[286] "stringi" "stringr" "survival"
[289] "sys" "sysfonts" "Tax4Fun"
[292] "tcltk" "tensorA" "testthat"
[295] "tibble" "tidygraph" "tidyr"
[298] "tidyselect" "tidytree" "tidyverse"
[301] "timeDate" "tinytex" "tools"
[304] "treeio" "tseries" "TTR"
[307] "tweenr" "UpSetR" "urca"
[310] "usethis" "utf8" "utils"
[313] "vctrs" "vegan" "VennDiagram"
[316] "venneuler" "viridis" "viridisLite"
[319] "webshot" "WGCNA" "whisker"
[322] "withr" "xfun" "xlsx"
[325] "xlsxjars" "XML" "xml2"
[328] "xopen" "xtable" "xts"
[331] "yaml" "yyplot" "zeallot"
[334] "zip" "zoo"