find a file under the current directoryfind ./ -name file_namefind files containing a phrase under the current directory: grep -rnw './' -e 'Bio::PrimarySeq' r: recursive; n:line number; w: match the whole word.
ggbiplot is good for plotting PCA result. However, it cannot be installed using the R function of install.packages. The github repository provides the installation commands as library(devtools)install_github("vqv/ggbiplot") But I ran into a new error message, saying "package install_github is not available (for R version 3.6.3)". I learned that base R did not have the function of install_github. The following code solved the issue.remotes::install_github('vqv/ggbiplot')
"The Ultimate vimrc" is a nice script for vim color scheme. To install the script, type the codes in terminal under your home folder git clone --depth=1 https://github.com/amix/vimrc.git ~/.vim_runtimesh ~/.vim_runtime/install_awesome_vimrc.shYou may also download the script here,vimrc.tar.gz. You need to move this tar file to your home folder before you decompress the file. Type the commands below under your home folder to install the vim color scheme tar -xvzf vimrc.tar.gz #decompress the file into a hidden folder ".vim_runtime"cd .vim_runtime #enter the hidden foldersh install_awesome_vimrc.sh
"qPrimerDB" is a useful webserver to simplify your qPCR primer design in a wide range of species. You may download the entire qPCR primer database for an organism of your interest and retrieve batch primer information using R For example, the best qPCR primer databases for Arabidopsis thaliana and Oryza sataiva Nipponbare are included in Ath_best_qPDB.txt and Osa_best_qDB.txt, respectively. To retrieve the qPCR primers of 15 A. thaliana F-box loci listed in a column of a tab file,target_loci.tab, you can download Ath_best_qPDB.txt to the same folder of target_loci.tab, and run the following simple R scripts under the same folder to get the primer sequences. database<-read.table("Ath_best_qPDB.txt",header=T) # read in the qPCR databaselist<-read.table("target_loci.tab",header=F) #read in the list of your target genesprimers<-database[database$GeneID %in% list[,1],] #find the information of your target loci write.csv(primers,"primer.csv") #saved in a CSV file
A great genomics blog
I accidentally discovered a good blog in genomics today. We may learn a lot from reading DAVE TANG'S BLOG. A good way to learn bioinformatics programming is to read other people's scripts for real projects.
Trouble in installing Hmisc
>install.packages("Hmisc") may result in a trouble showing belowmake: 77: No such file or directorymake: *** [cidxcn.o] Error 1ERROR: compilation failed for package HmiscOne might want to use Fink to install Hmisc. Unfortunately, it may run into the problem in failing installation of cran-stringi-r36. The error message of make: 77: No such file or directoryresults from the failure of finding gfortran. To solve this issue, use the code recommended by chlee-tabin as follows by editing Makevars file under the folder ~/.R.#FC=$F77 # comment out thisFC=/usr/local/bin/gfortran # insert this line instead
cran-stringi-r36 cannot be compiled
fink install cran-stringi-r36 produces an error message Error: package or namespace load failed for 'stringi' in dyn.load(file, DLLpath = DLLpath, ...):ICU init failed: U_FILE_ACCESS_ERROR This is caused by the the ICU4C library, on which stringi is based. To make it simple, use R to install stringi with a command as followssudo R CMD INSTALL --configure-args='--disable-pkg-config'This allows ./configure to use ICU4C bundle that comes with the package.
Fink makes R easy to install
Many may like R-studio. It is easy to install and has Integrated Development Environment (IDE). However, I personally don't like the IDE function. Just like Adobe Dreamweaver, I was really tired to switch different interfaces in using Dreamweaver to make a website. Since I learned HTML and CSS,I have removed Dreamweaver from my computer. To install R from source, it may experience trouble in compiling gfortran which R requires. Fortunately, Fink has the source repositories for both packages. Installing R could be done as easy as typing the code below in terminalfink list r-base #to list the list of R repositoriesfink install r-base36 #install R (version 3.6.3 in this case)
Fink is my favorite source repository for bioinformatics programs. Unfortunately, it was not working well on macOS from EI Capitan to Mojava. During that period, I shifted to Homebrew. I personally feel that brew does not cover as many packages as Fink does. I revisisted Fink today and I was happy to know it worked again. For macOS Mojave (v10.14.6), I used the helper script Install Fink 0.45.1 to install Fink