library("RVA")
install.packages("RVA")
.libPaths(
)
install.packages("RVA")
.libPaths()
.libPaths(c(.libPaths(), '/Users/pengzhizhang/.Rlib'))
.libPaths()
.libPaths(c(.libPaths(), '/Users/pengzhizhang/.Rlib'))
.libPaths()
install.packages("RVA", lib="/Users/pengzhizhang/.Rlib")
install.packages("RVA", lib="/Users/pengzhizhang/.Rlib")
install.packages("RVA", lib="/Users/pengzhizhang/.Rlib")
install.packages("RVA", lib="/Users/pengzhizhang/.Rlib")
help("install.packages")
options(install.packages.check.source = "yes")
install.packages("RVA", lib="/Users/pengzhizhang/.Rlib")
install.packages("RVA", lib="/Users/pengzhizhang/.Rlib", clean)
install.packages("RVA", lib="/Users/pengzhizhang/.Rlib", clean=True)
install.packages("RVA", lib="/Users/pengzhizhang/.Rlib", clean=TRUE)
devtools::install_github("THERMOSTATS/RVA_prod")
install.packages("~/RVA-master.zip", repos = NULL, type = "win.binary", lib="/Users/pengzhizhang/.Rlib")
install.packages("~/RVA-master.tgz", repos = NULL, type = .Platform$pkgType, lib="/Users/pengzhizhang/.Rlib")
install.packages("RVA", lib="/Users/pengzhizhang/.Rlib")
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("edgeR")
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("edgeR", lib="/Users/pengzhizhang/.Rlib")
install.packages("RVA", lib="/Users/pengzhizhang/.Rlib")
library("enhancedvolcano")
BiocManager::install('EnhancedVolcano')
.libPaths()
BiocManager::install('EnhancedVolcano')
q()
BiocManager::install("EnhancedVolcano")
library(EnhancedVolcano)
install.packages("tibble")
install.packages("tibble")
q()
install.packages("tibble")
install.packages("tibble", dependencies = None)
install.packages("tibble", dependencies = Null)
install.packages("tibble", dependencies = NULL)
install.packages("tibble", dependencies = NULL)
install.packages("glue", dependencies = NULL)
library(EnhancedVolcano)
library(ellipsis)
install.packages("ellipsis")
install.packages("ellipsis")
install.packages("ellipsis")
library(ellipsis)
.libPaths()
.libPaths("/Users/pengzhizhang/.Rlib")
library(ellipsis)
remove.packages("ellipsis", lib="~/.Rlib")
remove.packages("ellipsis", lib="/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
remove.packages("ellipsis", lib="/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
BiocManager::install("EnhancedVolcano")
library("EnhancedVolcano")
BiocManager::install("EnhancedVolcano", lib=.libPaths())
install.packages("BiocManager")
BiocManager::install("EnhancedVolcano", lib=.libPaths())
library(EnhancedVolcano)
install.packages(c("bbmle", "bdsmatrix", "BH", "BiocManager", "bit", "bit64", "bitops", "blob", "boot", "brew", "Cairo", "callr", "caTools", "changepoint", "checkmate", "class", "cli", "clipr", "cluster", "coda", "codetools", "colorspace", "commonmark", "covr", "cowplot", "crayon", "crosstalk", "curl", "data.table", "DBI", "desc", "devtools", "dichromat", "digest", "doMC", "doParallel", "dplyr", "DT", "ellipsis", "emdbook", "evaluate", "fansi", "farver", "fastmap", "foreach", "formatR", "Formula", "fs", "gdata", "gert", "ggplot2", "gh", "git2r", "glue", "gplots", "gtools", "hexbin", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "interp", "IRdisplay", "iterators", "jpeg", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "latticeExtra", "lifecycle", "lme4", "lubridate", "magrittr", "maptools", "MASS", "Matrix", "matrixStats", "memoise", "mgcv", "mime", "mvtnorm", "nlme", "nloptr", "nnet", "openssl", "openxlsx", "optparse", "outliers", "pbapply", "pillar", "pkgbuild", "pkgload", "plotly", "plyr", "prettyunits", "processx", "promises", "proxy", "ps", "purrr", "quantreg", "R6", "rcmdcheck", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "readr", "readxl", "remotes", "repr", "reshape2", "rex", "rgeos", "rlang", "rmarkdown", "roxygen2", "rpart", "rprojroot", "RSQLite", "rstudioapi", "rsvg", "rversions", "sass", "scales", "sessioninfo", "shiny", "snow", "sp", "spatial", "statmod", "stringi", "survival", "sys", "testthat", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "usethis", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xml2", "yaml", "zip", "zoo"), lib="/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
install.packages(c("bbmle", "bdsmatrix", "BH", "BiocManager", "bit", "bit64", "bitops", "blob", "boot", "brew", "Cairo", "callr", "caTools", "changepoint", "checkmate", "class", "cli", "clipr", "cluster", "coda", "codetools", "colorspace", "commonmark", "covr", "cowplot", "crayon", "crosstalk", "curl", "data.table", "DBI", "desc", "devtools", "dichromat", "digest", "doMC", "doParallel", "dplyr", "DT", "ellipsis", "emdbook", "evaluate", "fansi", "farver", "fastmap", "foreach", "formatR", "Formula", "fs", "gdata", "gert", "ggplot2", "gh", "git2r", "glue", "gplots", "gtools", "hexbin", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "interp", "IRdisplay", "iterators", "jpeg", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "latticeExtra", "lifecycle", "lme4", "lubridate", "magrittr", "maptools", "MASS", "Matrix", "matrixStats", "memoise", "mgcv", "mime", "mvtnorm", "nlme", "nloptr", "nnet", "openssl", "openxlsx", "optparse", "outliers", "pbapply", "pillar", "pkgbuild", "pkgload", "plotly", "plyr", "prettyunits", "processx", "promises", "proxy", "ps", "purrr", "quantreg", "R6", "rcmdcheck", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "readr", "readxl", "remotes", "repr", "reshape2", "rex", "rgeos", "rlang", "rmarkdown", "roxygen2", "rpart", "rprojroot", "RSQLite", "rstudioapi", "rsvg", "rversions", "sass", "scales", "sessioninfo", "shiny", "snow", "sp", "spatial", "statmod", "stringi", "survival", "sys", "testthat", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "usethis", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xml2", "yaml", "zip", "zoo"), lib = "/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
install.packages(c("bbmle", "bdsmatrix", "BH", "BiocManager", "bit", "bit64", "bitops", "blob", "boot", "brew", "Cairo", "callr", "caTools", "changepoint", "checkmate", "class", "cli", "clipr", "cluster", "coda", "codetools", "colorspace", "commonmark", "covr", "cowplot", "crayon", "crosstalk", "curl", "data.table", "DBI", "desc", "devtools", "dichromat", "digest", "doMC", "doParallel", "dplyr", "DT", "ellipsis", "emdbook", "evaluate", "fansi", "farver", "fastmap", "foreach", "formatR", "Formula", "fs", "gdata", "gert", "ggplot2", "gh", "git2r", "glue", "gplots", "gtools", "hexbin", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "interp", "IRdisplay", "iterators", "jpeg", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "latticeExtra", "lifecycle", "lme4", "lubridate", "magrittr", "maptools", "MASS", "Matrix", "matrixStats", "memoise", "mgcv", "mime", "mvtnorm", "nlme", "nloptr", "nnet", "openssl", "openxlsx", "optparse", "outliers", "pbapply", "pillar", "pkgbuild", "pkgload", "plotly", "plyr", "prettyunits", "processx", "promises", "proxy", "ps", "purrr", "quantreg", "R6", "rcmdcheck", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "readr", "readxl", "remotes", "repr", "reshape2", "rex", "rgeos", "rlang", "rmarkdown", "roxygen2", "rpart", "rprojroot", "RSQLite", "rstudioapi", "rsvg", "rversions", "sass", "scales", "sessioninfo", "shiny", "snow", "sp", "spatial", "statmod", "stringi", "survival", "sys", "testthat", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "usethis", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xml2", "yaml", "zip", "zoo"), lib = "/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
install.packages(c("bbmle", "bdsmatrix", "BH", "BiocManager", "bit", "bit64", "bitops", "blob", "boot", "brew", "Cairo", "callr", "caTools", "changepoint", "checkmate", "class", "cli", "clipr", "cluster", "coda", "codetools", "colorspace", "commonmark", "covr", "cowplot", "crayon", "crosstalk", "curl", "data.table", "DBI", "desc", "devtools", "dichromat", "digest", "doMC", "doParallel", "dplyr", "DT", "ellipsis", "emdbook", "evaluate", "fansi", "farver", "fastmap", "foreach", "formatR", "Formula", "fs", "gdata", "gert", "ggplot2", "gh", "git2r", "glue", "gplots", "gtools", "hexbin", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "interp", "IRdisplay", "iterators", "jpeg", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "latticeExtra", "lifecycle", "lme4", "lubridate", "magrittr", "maptools", "MASS", "Matrix", "matrixStats", "memoise", "mgcv", "mime", "mvtnorm", "nlme", "nloptr", "nnet", "openssl", "openxlsx", "optparse", "outliers", "pbapply", "pillar", "pkgbuild", "pkgload", "plotly", "plyr", "prettyunits", "processx", "promises", "proxy", "ps", "purrr", "quantreg", "R6", "rcmdcheck", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "readr", "readxl", "remotes", "repr", "reshape2", "rex", "rgeos", "rlang", "rmarkdown", "roxygen2", "rpart", "rprojroot", "RSQLite", "rstudioapi", "rsvg", "rversions", "sass", "scales", "sessioninfo", "shiny", "snow", "sp", "spatial", "statmod", "stringi", "survival", "sys", "testthat", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "usethis", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xml2", "yaml", "zip", "zoo"), lib = "/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
install.packages(c("bbmle", "bdsmatrix", "BH", "BiocManager", "bit", "bit64", "bitops", "blob", "boot", "brew", "Cairo", "callr", "caTools", "changepoint", "checkmate", "class", "cli", "clipr", "cluster", "coda", "codetools", "colorspace", "commonmark", "covr", "cowplot", "crayon", "crosstalk", "curl", "data.table", "DBI", "desc", "devtools", "dichromat", "digest", "doMC", "doParallel", "dplyr", "DT", "ellipsis", "emdbook", "evaluate", "fansi", "farver", "fastmap", "foreach", "formatR", "Formula", "fs", "gdata", "gert", "ggplot2", "gh", "git2r", "glue", "gplots", "gtools", "hexbin", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "interp", "IRdisplay", "iterators", "jpeg", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "latticeExtra", "lifecycle", "lme4", "lubridate", "magrittr", "maptools", "MASS", "Matrix", "matrixStats", "memoise", "mgcv", "mime", "mvtnorm", "nlme", "nloptr", "nnet", "openssl", "openxlsx", "optparse", "outliers", "pbapply", "pillar", "pkgbuild", "pkgload", "plotly", "plyr", "prettyunits", "processx", "promises", "proxy", "ps", "purrr", "quantreg", "R6", "rcmdcheck", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "readr", "readxl", "remotes", "repr", "reshape2", "rex", "rgeos", "rlang", "rmarkdown", "roxygen2", "rpart", "rprojroot", "RSQLite", "rstudioapi", "rsvg", "rversions", "sass", "scales", "sessioninfo", "shiny", "snow", "sp", "spatial", "statmod", "stringi", "survival", "sys", "testthat", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "usethis", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xml2", "yaml", "zip", "zoo"), lib = "/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
install.packages(c("bbmle", "bdsmatrix", "BH", "BiocManager", "bit", "bit64", "bitops", "blob", "boot", "brew", "Cairo", "callr", "caTools", "changepoint", "checkmate", "class", "cli", "clipr", "cluster", "coda", "codetools", "colorspace", "commonmark", "covr", "cowplot", "crayon", "crosstalk", "curl", "data.table", "DBI", "desc", "devtools", "dichromat", "digest", "doMC", "doParallel", "dplyr", "DT", "ellipsis", "emdbook", "evaluate", "fansi", "farver", "fastmap", "foreach", "formatR", "Formula", "fs", "gdata", "gert", "ggplot2", "gh", "git2r", "glue", "gplots", "gtools", "hexbin", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "interp", "IRdisplay", "iterators", "jpeg", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "latticeExtra", "lifecycle", "lme4", "lubridate", "magrittr", "maptools", "MASS", "Matrix", "matrixStats", "memoise", "mgcv", "mime", "mvtnorm", "nlme", "nloptr", "nnet", "openssl", "openxlsx", "optparse", "outliers", "pbapply", "pillar", "pkgbuild", "pkgload", "plotly", "plyr", "prettyunits", "processx", "promises", "proxy", "ps", "purrr", "quantreg", "R6", "rcmdcheck", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "readr", "readxl", "remotes", "repr", "reshape2", "rex", "rgeos", "rlang", "rmarkdown", "roxygen2", "rpart", "rprojroot", "RSQLite", "rstudioapi", "rsvg", "rversions", "sass", "scales", "sessioninfo", "shiny", "snow", "sp", "spatial", "statmod", "stringi", "survival", "sys", "testthat", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "usethis", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xml2", "yaml", "zip", "zoo"), lib = "/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
install.packages(c("bbmle", "bdsmatrix", "BH", "BiocManager", "bit", "bit64", "bitops", "blob", "boot", "brew", "Cairo", "callr", "caTools", "changepoint", "checkmate", "class", "cli", "clipr", "cluster", "coda", "codetools", "colorspace", "commonmark", "covr", "cowplot", "crayon", "crosstalk", "curl", "data.table", "DBI", "desc", "devtools", "dichromat", "digest", "doMC", "doParallel", "dplyr", "DT", "ellipsis", "emdbook", "evaluate", "fansi", "farver", "fastmap", "foreach", "formatR", "Formula", "fs", "gdata", "gert", "ggplot2", "gh", "git2r", "glue", "gplots", "gtools", "hexbin", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "interp", "IRdisplay", "iterators", "jpeg", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "latticeExtra", "lifecycle", "lme4", "lubridate", "magrittr", "maptools", "MASS", "Matrix", "matrixStats", "memoise", "mgcv", "mime", "mvtnorm", "nlme", "nloptr", "nnet", "openssl", "openxlsx", "optparse", "outliers", "pbapply", "pillar", "pkgbuild", "pkgload", "plotly", "plyr", "prettyunits", "processx", "promises", "proxy", "ps", "purrr", "quantreg", "R6", "rcmdcheck", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "readr", "readxl", "remotes", "repr", "reshape2", "rex", "rgeos", "rlang", "rmarkdown", "roxygen2", "rpart", "rprojroot", "RSQLite", "rstudioapi", "rsvg", "rversions", "sass", "scales", "sessioninfo", "shiny", "snow", "sp", "spatial", "statmod", "stringi", "survival", "sys", "testthat", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "usethis", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xml2", "yaml", "zip", "zoo"), lib = "/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
install.packages(c("bbmle", "bdsmatrix", "BH", "BiocManager", "bit", "bit64", "bitops", "blob", "boot", "brew", "Cairo", "callr", "caTools", "changepoint", "checkmate", "class", "cli", "clipr", "cluster", "coda", "codetools", "colorspace", "commonmark", "covr", "cowplot", "crayon", "crosstalk", "curl", "data.table", "DBI", "desc", "devtools", "dichromat", "digest", "doMC", "doParallel", "dplyr", "DT", "ellipsis", "emdbook", "evaluate", "fansi", "farver", "fastmap", "foreach", "formatR", "Formula", "fs", "gdata", "gert", "ggplot2", "gh", "git2r", "glue", "gplots", "gtools", "hexbin", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "interp", "IRdisplay", "iterators", "jpeg", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "latticeExtra", "lifecycle", "lme4", "lubridate", "magrittr", "maptools", "MASS", "Matrix", "matrixStats", "memoise", "mgcv", "mime", "mvtnorm", "nlme", "nloptr", "nnet", "openssl", "openxlsx", "optparse", "outliers", "pbapply", "pillar", "pkgbuild", "pkgload", "plotly", "plyr", "prettyunits", "processx", "promises", "proxy", "ps", "purrr", "quantreg", "R6", "rcmdcheck", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "readr", "readxl", "remotes", "repr", "reshape2", "rex", "rgeos", "rlang", "rmarkdown", "roxygen2", "rpart", "rprojroot", "RSQLite", "rstudioapi", "rsvg", "rversions", "sass", "scales", "sessioninfo", "shiny", "snow", "sp", "spatial", "statmod", "stringi", "survival", "sys", "testthat", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "usethis", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xml2", "yaml", "zip", "zoo"), lib = "/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
install.packages(c("bbmle", "bdsmatrix", "BH", "BiocManager", "bit", "bit64", "bitops", "blob", "boot", "brew", "Cairo", "callr", "caTools", "changepoint", "checkmate", "class", "cli", "clipr", "cluster", "coda", "codetools", "colorspace", "commonmark", "covr", "cowplot", "crayon", "crosstalk", "curl", "data.table", "DBI", "desc", "devtools", "dichromat", "digest", "doMC", "doParallel", "dplyr", "DT", "ellipsis", "emdbook", "evaluate", "fansi", "farver", "fastmap", "foreach", "formatR", "Formula", "fs", "gdata", "gert", "ggplot2", "gh", "git2r", "glue", "gplots", "gtools", "hexbin", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "interp", "IRdisplay", "iterators", "jpeg", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "latticeExtra", "lifecycle", "lme4", "lubridate", "magrittr", "maptools", "MASS", "Matrix", "matrixStats", "memoise", "mgcv", "mime", "mvtnorm", "nlme", "nloptr", "nnet", "openssl", "openxlsx", "optparse", "outliers", "pbapply", "pillar", "pkgbuild", "pkgload", "plotly", "plyr", "prettyunits", "processx", "promises", "proxy", "ps", "purrr", "quantreg", "R6", "rcmdcheck", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "readr", "readxl", "remotes", "repr", "reshape2", "rex", "rgeos", "rlang", "rmarkdown", "roxygen2", "rpart", "rprojroot", "RSQLite", "rstudioapi", "rsvg", "rversions", "sass", "scales", "sessioninfo", "shiny", "snow", "sp", "spatial", "statmod", "stringi", "survival", "sys", "testthat", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "usethis", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xml2", "yaml", "zip", "zoo"), lib = "/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
install.packages(c("bbmle", "bdsmatrix", "BH", "BiocManager", "bit", "bit64", "bitops", "blob", "boot", "brew", "Cairo", "callr", "caTools", "changepoint", "checkmate", "class", "cli", "clipr", "cluster", "coda", "codetools", "colorspace", "commonmark", "covr", "cowplot", "crayon", "crosstalk", "curl", "data.table", "DBI", "desc", "devtools", "dichromat", "digest", "doMC", "doParallel", "dplyr", "DT", "ellipsis", "emdbook", "evaluate", "fansi", "farver", "fastmap", "foreach", "formatR", "Formula", "fs", "gdata", "gert", "ggplot2", "gh", "git2r", "glue", "gplots", "gtools", "hexbin", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "interp", "IRdisplay", "iterators", "jpeg", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "latticeExtra", "lifecycle", "lme4", "lubridate", "magrittr", "maptools", "MASS", "Matrix", "matrixStats", "memoise", "mgcv", "mime", "mvtnorm", "nlme", "nloptr", "nnet", "openssl", "openxlsx", "optparse", "outliers", "pbapply", "pillar", "pkgbuild", "pkgload", "plotly", "plyr", "prettyunits", "processx", "promises", "proxy", "ps", "purrr", "quantreg", "R6", "rcmdcheck", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "readr", "readxl", "remotes", "repr", "reshape2", "rex", "rgeos", "rlang", "rmarkdown", "roxygen2", "rpart", "rprojroot", "RSQLite", "rstudioapi", "rsvg", "rversions", "sass", "scales", "sessioninfo", "shiny", "snow", "sp", "spatial", "statmod", "stringi", "survival", "sys", "testthat", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "usethis", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xml2", "yaml", "zip", "zoo"), lib = "/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
install.packages(c("bbmle", "bdsmatrix", "BH", "BiocManager", "bit", "bit64", "bitops", "blob", "boot", "brew", "Cairo", "callr", "caTools", "changepoint", "checkmate", "class", "cli", "clipr", "cluster", "coda", "codetools", "colorspace", "commonmark", "covr", "cowplot", "crayon", "crosstalk", "curl", "data.table", "DBI", "desc", "devtools", "dichromat", "digest", "doMC", "doParallel", "dplyr", "DT", "ellipsis", "emdbook", "evaluate", "fansi", "farver", "fastmap", "foreach", "formatR", "Formula", "fs", "gdata", "gert", "ggplot2", "gh", "git2r", "glue", "gplots", "gtools", "hexbin", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "interp", "IRdisplay", "iterators", "jpeg", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "latticeExtra", "lifecycle", "lme4", "lubridate", "magrittr", "maptools", "MASS", "Matrix", "matrixStats", "memoise", "mgcv", "mime", "mvtnorm", "nlme", "nloptr", "nnet", "openssl", "openxlsx", "optparse", "outliers", "pbapply", "pillar", "pkgbuild", "pkgload", "plotly", "plyr", "prettyunits", "processx", "promises", "proxy", "ps", "purrr", "quantreg", "R6", "rcmdcheck", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "readr", "readxl", "remotes", "repr", "reshape2", "rex", "rgeos", "rlang", "rmarkdown", "roxygen2", "rpart", "rprojroot", "RSQLite", "rstudioapi", "rsvg", "rversions", "sass", "scales", "sessioninfo", "shiny", "snow", "sp", "spatial", "statmod", "stringi", "survival", "sys", "testthat", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "usethis", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xml2", "yaml", "zip", "zoo"), lib = "/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
install.packages(c("bbmle", "bdsmatrix", "BH", "BiocManager", "bit", "bit64", "bitops", "blob", "boot", "brew", "Cairo", "callr", "caTools", "changepoint", "checkmate", "class", "cli", "clipr", "cluster", "coda", "codetools", "colorspace", "commonmark", "covr", "cowplot", "crayon", "crosstalk", "curl", "data.table", "DBI", "desc", "devtools", "dichromat", "digest", "doMC", "doParallel", "dplyr", "DT", "ellipsis", "emdbook", "evaluate", "fansi", "farver", "fastmap", "foreach", "formatR", "Formula", "fs", "gdata", "gert", "ggplot2", "gh", "git2r", "glue", "gplots", "gtools", "hexbin", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "interp", "IRdisplay", "iterators", "jpeg", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "latticeExtra", "lifecycle", "lme4", "lubridate", "magrittr", "maptools", "MASS", "Matrix", "matrixStats", "memoise", "mgcv", "mime", "mvtnorm", "nlme", "nloptr", "nnet", "openssl", "openxlsx", "optparse", "outliers", "pbapply", "pillar", "pkgbuild", "pkgload", "plotly", "plyr", "prettyunits", "processx", "promises", "proxy", "ps", "purrr", "quantreg", "R6", "rcmdcheck", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "readr", "readxl", "remotes", "repr", "reshape2", "rex", "rgeos", "rlang", "rmarkdown", "roxygen2", "rpart", "rprojroot", "RSQLite", "rstudioapi", "rsvg", "rversions", "sass", "scales", "sessioninfo", "shiny", "snow", "sp", "spatial", "statmod", "stringi", "survival", "sys", "testthat", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "usethis", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xml2", "yaml", "zip", "zoo"), lib="/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
BiocManager::install("EnhancedVolcano")
.libPaths()
usethis::edit_r_profile()
exit
exit()
quit()
BiocManager::install("EnhancedVolcano")
usethis::edit_r_profile()
source('~/.Rprofile')
source('~/.Rprofile')
source('~/.Rprofile')
.libPaths()
source('~/.Rprofile')
.libPaths("/Users/")
.libPaths()
.libPaths()
source('~/.Rprofile')
.libPaths()
plot(cars)
if (!require(BiocManager)) {
install.packages("BiocManager")
}
BiocManager::install(c("DropletUtils", "BUSpaRse"))
if (!require(BiocManager)) {
install.packages("BiocManager")
}
BiocManager::install(c("BUSpaRse"))
if (!require(BiocManager)) {
install.packages("BiocManager")
}
BiocManager::install(c("BUSpaRse"))
if (!require(BiocManager)) {
install.packages("BiocManager")
}
BiocManager::install(c("BUSpaRse"))
.path.package()
path.package()
path.package("bdsmatrix")
.libPaths()
if (!require(BiocManager)) {
install.packages("BiocManager")
}
BiocManager::install(c("BUSpaRse"))
.libPaths()
.libPaths()
if (!require(BiocManager)) {
install.packages("BiocManager")
}
BiocManager::install(c("BUSpaRse"))
install.packages("BH")
install.packages(c("bbmle", "bdsmatrix", "BH", "BiocManager", "bit", "bit64", "bitops", "blob", "boot", "brew", "Cairo", "callr", "caTools", "changepoint", "checkmate", "class", "cli", "clipr", "cluster", "coda", "codetools", "colorspace", "commonmark", "covr", "cowplot", "crayon", "crosstalk", "curl", "data.table", "DBI", "desc", "devtools", "dichromat", "digest", "doMC", "doParallel", "dplyr", "DT", "ellipsis", "emdbook", "evaluate", "fansi", "farver", "fastmap", "fontawesome", "foreach", "formatR", "Formula", "fs", "gdata", "gert", "ggplot2", "gh", "git2r", "glue", "gplots", "gtools", "hexbin", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "interp", "IRdisplay", "iterators", "jpeg", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "latticeExtra", "lifecycle", "lme4", "lubridate", "magrittr", "maptools", "MASS", "Matrix", "matrixStats", "memoise", "mgcv", "mime", "mvtnorm", "nlme", "nloptr", "nnet", "openssl", "openxlsx", "optparse", "outliers", "pbapply", "pillar", "pkgbuild", "pkgload", "plotly", "plyr", "prettyunits", "processx", "promises", "proxy", "ps", "purrr", "quantreg", "R6", "ragg", "rcmdcheck", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "readr", "readxl", "remotes", "repr", "reshape2", "rex", "rgeos", "rlang", "rmarkdown", "roxygen2", "rpart", "rprojroot", "RSQLite", "rstudioapi", "rsvg", "rversions", "sass", "scales", "sessioninfo", "shiny", "snow", "sp", "spatial", "statmod", "stringi", "survival", "sys", "systemfonts", "testthat", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "usethis", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xml2", "yaml", "zip", "zoo"))
library(BH)
install.packages("BH")
install.packages("BH")
install.packages("BH")
install.packages("BH")
install.packages("BH")
install.packages(c("bbmle", "bdsmatrix", "BiocManager", "bit", "bit64", "bitops", "blob", "boot", "brew", "Cairo", "callr", "caTools", "changepoint", "checkmate", "class", "cli", "clipr", "cluster", "coda", "codetools", "colorspace", "commonmark", "covr", "cowplot", "crayon", "crosstalk", "curl", "data.table", "DBI", "desc", "devtools", "dichromat", "digest", "doMC", "doParallel", "dplyr", "DT", "ellipsis", "emdbook", "evaluate", "fansi", "farver", "fastmap", "fontawesome", "foreach", "formatR", "Formula", "fs", "gdata", "gert", "ggplot2", "gh", "git2r", "glue", "gplots", "gtools", "hexbin", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "interp", "IRdisplay", "iterators", "jpeg", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "latticeExtra", "lifecycle", "lme4", "lubridate", "magrittr", "maptools", "MASS", "Matrix", "matrixStats", "memoise", "mgcv", "mime", "mvtnorm", "nlme", "nloptr", "nnet", "openssl", "openxlsx", "optparse", "outliers", "pbapply", "pillar", "pkgbuild", "pkgload", "plotly", "plyr", "prettyunits", "processx", "promises", "proxy", "ps", "purrr", "quantreg", "R6", "ragg", "rcmdcheck", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "readr", "readxl", "remotes", "repr", "reshape2", "rex", "rgeos", "rlang", "rmarkdown", "roxygen2", "rpart", "rprojroot", "RSQLite", "rstudioapi", "rsvg", "rversions", "sass", "scales", "sessioninfo", "shiny", "snow", "sp", "spatial", "statmod", "stringi", "survival", "sys", "systemfonts", "testthat", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "usethis", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xml2", "yaml", "zip", "zoo"))
install.packages(c("cluster", "gert", "Hmisc", "interp", "Matrix", "mgcv", "nlme", "nloptr", "quantreg", "RcppArmadillo", "RcppEigen", "rsvg"))
BiocManager::install(c("BUSpaRse"))
install.packages("cluster")
install.packages(c("cluster", "gert", "Hmisc", "interp", "Matrix", "mgcv", "nlme", "nloptr", "quantreg", "RcppArmadillo", "RcppEigen", "rsvg"))
BiocManager::install(c("BUSpaRse"))
BiocManager::install("BUSpaRse")
library(devtools)
install_github('andreacirilloac/updateR')
library(updateR)
updateR
exit
exit9)
quit()
if (!require(BiocManager)) {
install.packages("BiocManager")
}
BiocManager::install(c("DropletUtils", "BUSpaRse"))
BiocManager::install(c("DropletUtils", "BUSpaRse"))
library(BUSpaRse)
library(DropletUtils)
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("edgeR")
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("edgeR")
library(DropletUtils)
list.files("./OneSRA/kallisto_count/
")"
list.files("./OneSRA/kallisto_count/counts_unfiltered/")
res_mat <- read_count_output("./OneSRA/kallisto_count/counts_unfiltered/",
name = "cells_x_tcc", tcc = TRUE)
res_mat
dim(res_mat)
tot_counts <- Matrix::colSums(res_mat)
summary(tot_counts)
bc_rank <- barcodeRanks(res_mat)
qplot(bc_rank$total, bc_rank$rank, geom = "line") +
geom_vline(xintercept = metadata(bc_rank)$knee, color = "blue", linetype = 2) +
geom_vline(xintercept = metadata(bc_rank)$inflection, color = "green", linetype = 2) +
annotate("text", y = 1000, x = 1.5 * c(metadata(bc_rank)$knee, metadata(bc_rank)$inflection),
label = c("knee", "inflection"), color = c("blue", "green")) +
scale_x_log10() +
scale_y_log10() +
labs(y = "Barcode rank", x = "Total UMI count")
install.packages(tidyverse)
install.packages("tidyverse")
library(tidyverse)
qplot(bc_rank$total, bc_rank$rank, geom = "line") +
geom_vline(xintercept = metadata(bc_rank)$knee, color = "blue", linetype = 2) +
geom_vline(xintercept = metadata(bc_rank)$inflection, color = "green", linetype = 2) +
annotate("text", y = 1000, x = 1.5 * c(metadata(bc_rank)$knee, metadata(bc_rank)$inflection),
label = c("knee", "inflection"), color = c("blue", "green")) +
scale_x_log10() +
scale_y_log10() +
labs(y = "Barcode rank", x = "Total UMI count")
help(make_sparse_matrix)
res_mat
make_sparse_matrix(bus_path="./OneSRA/kallisto_count/counts_unfiltered/")
make_sparse_matrix(bus_path="KBtools-test//OneSRA/kallisto_count/counts_unfiltered/")
make_sparse_matrix(bus_path="KBtools-test/OneSRA/kallisto_count/counts_unfiltered/")
make_sparse_matrix(bus_path="KBtools-test/OneSRA/kallisto_count/counts_unfiltered/cells_x_tcc.mtx")
make_sparse_matrix(bus_path="KBtools-test/OneSRA/kallisto_count/output.unfiltered.bus")
make_sparse_matrix(bus_path="KBtools-test/OneSRA/kallisto_count/output.bus")
make_sparse_matrix(bus_path="KBtools-test/OneSRA/kallisto_count/matrix.ec")
library(TENxBUSData)
BiocManager::install("TENxBUSData")
TENxBUSData(".", dataset = "hgmm100")
library(TENxBUSData)
TENxBUSData(".", dataset = "hgmm100")
bustools
install.packages(c("BH", "BiocManager", "boot", "broom", "bslib", "class", "cli", "codetools", "colorspace", "curl", "digest", "DT", "e1071", "evaluate", "fansi", "fontawesome", "forcats", "foreign", "formatR", "fs", "future", "gargle", "gert", "ggbeeswarm", "ggplot2", "ggpubr", "ggrepel", "googlesheets4", "haven", "hdf5r", "highr", "Hmisc", "hms", "httpuv", "igraph", "isoband", "jsonlite", "knitr", "leidenbase", "listenv", "locfit", "lubridate", "markdown", "MASS", "Matrix", "modelr", "nlme", "NMF", "openssl", "parallelly", "pbapply", "pbkrtest", "pkgbuild", "pkgdown", "pkgmaker", "progressr", "R.utils", "ragg", "Rcpp", "RcppTOML", "RCurl", "readr", "readxl", "reprex", "reticulate", "RhpcBLASctl", "rmarkdown", "roxygen2", "rsample", "RSQLite", "rstatix", "rstudioapi", "rvest", "s2", "sass", "shiny", "sourcetools", "sp", "spatstat.explore", "spatstat.geom", "spatstat.random", "stringi", "survival", "terra", "testthat", "tinytex", "units", "utf8", "vroom", "WGCNA", "whisker", "wk", "xfun", "XML", "yaml"))
suppressMessages(library("optparse"))
paste0("results", None, 1)
paste0("results", NULL, 1)
paste0("results/", NULL, "/1.csv")
file.path("usr", "local", "lib")
file.path("results", NULL, "1.csv")
file.path("results", "NULL", "1.csv")
dir.create
help(dir.create)
setwd("~/ST_Histo/src/analysis/")
source("~/ST_Histo/src/analysis/dend_plot.R")
hc <- readRDS("~/ST_Histo/src/analysis/SPARKX_cell_wd/y_smooth_20/hc.rds")
library(readr)
res_matrix <- read_csv("SPARKX_cell_wd/y_smooth_20/res_matrix.csv")
library(readr)
res_matrix <- read_csv("SPARKX_cell_wd/y_smooth_20/res_matrix.csv")
sig_vst_res_sc <- res_matrix
hc_sc <- hc
num <- 6
memb <- cutree(hc_sc, k = num)
gene = cbind.data.frame(gene = hc_sc$labels, cluster = memb)
write.table(gene, file.path 'gene_cluster_6.txt'), sep='\t', row.names = F, quote = F)
write.table(gene, file.path('gene_cluster_6.txt'), sep='\t', row.names = F, quote = F)
cent <- NULL
for (k in 1:num) {
cent <- cbind(cent, colMeans(sig_vst_res_sc[memb == k, , drop = FALSE]))
}
cbind(NULL, colMeans(sig_vst_res_sc[memb == k], drop=FALSE))
cbind(NULL, colMeans(sig_vst_res_sc[memb == 1], drop=FALSE))
help(colMeans)
cbind(NULL, colMeans(sig_vst_res_sc[memb == 1]), drop=FALSE))
cbind(NULL, colMeans(sig_vst_res_sc[memb == 1]), drop=FALSE)
colMeans(sig_vst_res_sc[memb == 1])
memb
colMeans(sig_vst_res_sc[:,memb == 1])
colMeans(sig_vst_res_sc[,memb == 1])
colMeans(sig_vst_res_sc[,: memb == 1])
colMeans(sig_vst_res_sc[memb == 1])
help(colMeans)
sig_vst_res_sc <- res_matrix.T
sig_vst_res_sc <- t(sig_vst_res_sc)
View(hc)
View(res_matrix)
View(sig_vst_res_sc)
sig_vst_res_sc[memb == 1]
memb == 1
hc_sc <- hcluster(sig_vst_res_sc, method = "euc", link = "ward", nbproc = 1, doubleprecision = TRUE)
library(hcluster)
library("hcluster")
library("amap")
hc_sc <- hcluster(sig_vst_res_sc, method = "euc", link = "ward", nbproc = 1, doubleprecision = TRUE)
memb <- cutree(hc_sc, k = num)
gene = cbind.data.frame(gene = hc_sc$labels, cluster = memb)
memb
memb == 1
sig_vst_res_sc[memb == 1]
t(sig_vst_res_sc)[memb == 1]
library(readr)
mtcars <- mtcars
mtcars
write_csv(x = mtcars, "example-data/mtcars.csv")
write_csv(x = mtcars, "mtcars.csv")
a <- read_csv("mtcars.csv")
a
mtcars
a
read.csv('mtcars.csv')
write.csv(mtcars, "mtcars-2.csv")
hc <- read.csv("SPARKX_cell_6/y_smooth_20/res_matrix.csv")
hc
memb <- cutree(hc_sc, k = num)
cent <- NULL
for (k in 1:num) {
cent <- cbind(cent, colMeans(sig_vst_res_sc[memb == k, , drop = FALSE]))
}
sig_vst_res_sc = t(sig_vst_res_sc)
