.Rhistory

reticulate::repl_python()
reticulate::repl_python()
install.packages(reticulate)
install.packages('reticulate')
install.packages("reticulate")
library(reticulate)
reticulate::repl_python()
reticulate::repl_python()
install.packages('reticulate') # allows you to execute python code chunks in RStudio
library(reticulate)
reticulate::repl_python()
reticulate::repl_python()
reticulate::repl_python()
Sys.setenv(PATH = "~/miniconda3/bin:" Sys.getenv("PATH"))
Sys.setenv(PATH = "/home/shared/8TB_HDD_02/stanja/miniconda3/bin:" Sys.getenv("PATH"))
Sys.setenv(PATH = "/home/shared/8TB_HDD_02/stanja/miniconda3/bin:" Sys.getenv("PATH"))
Sys.setenv(PATH = paste("/home/shared/8TB_HDD_02/stanja/miniconda3/bin:", Sys.getenv("PATH"), sep = ":"))
conda list
# Execute conda list using system() function
system("conda list", intern = TRUE)
install.packages("IRkernel")
IRkernel::installspec()
IRkernel::installspec()
install.packages('IRkernel')
install.packages("IRkernel")
IRkernel::installspec()
devtools::install_github("jbisanz/qiime2R") # current version is 0.99.20
library(devtools)
if (!requireNamespace("devtools", quietly = TRUE)){install.packages("devtools")}
if (!requireNamespace("devtools", quietly = TRUE)){install.packages("devtools")}
devtools::install_github("jbisanz/qiime2R") # current version is 0.99.20
library(qiime2R)
ASV <- read_qza("../output/dada2/table.qza")
metadata<-read_q2metadata("../data/sample-metadata-verbose.tsv")
metadata <- read_q2metadata("../data/sample-metadata-verbose.tsv")
metadata <- read_tsv("../data/sample-metadata-verbose.tsv")
readr::read_tsv()
readr::read_tsv()
metadata <- readr::read_tsv("../data/sample-metadata-verbose.tsv")
head(metadata)
install.packages("qiime2R")
install.packages("qiime2R")
install.packages("Rtools")