I am trying to import geodatabase GSE files into R and I do not know how to get them in a format that can be analyzed by bioconductor software can you tell me how to do so?
Have you tried the GEOquery package? Be sure to read the vignette
Related
I am trying to schematic plot of txt data but when I write schematic.plot there is no package in Rstudio. I am searching for the package but it is not downloading.
In order to install a package in Rstudio you would want to run the command to in the console as follows:
install.packages("BiocManager")
To install ELMER as this package contains the schematic.plot function I believe you are looking for we actually install it using bioconductors installer as follows:
install.packages("BiocManager")
BiocManager::install("ELMER")
Please let me know if this isn't what you're looking for and I'll try to improve the answer.
You probably need to do:
install.packages("ELMER")
library(ELMER)
to get the package in there.
I have just built a function and planned to put it into Github. The problem is that my function uses a lot of other R packages (e.g., dplyr, tidyverse,...), leading to when people clone my package from Github to R using remotes::install_github, they will have to additionally install those packages (e.g., dplyr, tidyverse,...). I wish when they install my package, they can use my package immediately. In other words, is any way to let they be able to simultaneously install all those packages when installing my R package.
My potential solution is that I will create a separate RData file whose role is to install and call those R libraries. Does it work?
I am trying to download openNLPmodels.en package in R for Named Entity Recognition but failed to download it successfully. Please suggest any other package in R for NER other than the above.
Thank you in advance.
Though not on CRAN yet, I find entity package on GitHub useful for me. FYI: https://github.com/trinker/entity
If you want to do Named Entity Recognition with custom labels, you can use package crfsuite. https://cran.r-project.org/web//packages/crfsuite/index.html
I have spent the past several days trying to install RDCOMClient in order to integrate R output in MS Word using R2wd
Thanks to SO, I was finally able to wrestle devtools and other required packages into shape (man, that was way more difficult than it should have been!) but I have not been able to install RDCOMClient
The closest I have come is downloading RDCOMClient_0.93-0.zip and then receiving the error message
"Error: package ‘RDCOMClient’ was built before R 3.0.0: please
re-install it"
I also received the message
"package ‘RDCOMClient’ is not available (for R version 3.4.0)"
at one point.
I have tried the omegahat site as well as github and CRAN with no luck.
I am beginning to think the package is no longer available (I wish I had known that days ago!) but still wonder if I am missing something.
If the package is no longer available for version 3.4.0, can you suggest another package with similar functionality? I am looking to write analyses in MS Word and then embed tables, charts and other output from R.
Thanks!
Yes it is. You need to install Rtools first.
Then you can install RDCOMClient via:
remotes::install_github("omegahat/RDCOMClient")
I am using the "Mining Twitter for Airline Sentiment" tutorial to learn R. (tutorial at http://www.inside-r.org/howto/mining-twitter-airline-consumer-sentiment.)
The parsing algorithm requires loading the external "stringr" library. The R gui terminal consistently says it cannot find the library, even though multiple references exist online.
This is my first experience with an R tutorial. Any suggestions?
Thanks,
#brianpiercy
install.packages("stringr", repos='http://cran.us.r-project.org')
library("stringr")
DWin was right, learn more about "R Package" here.
You may try CloudStat: Twitter analysis.
Summary for newbie:
Go to stringr | Cran-R download the source file. Through your R Gui:
Packages > Install Package(s) from local zip file
Then, Load the library
library(stringr)
Hope it help.