Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/czheluo/r-script
R Script for research
https://github.com/czheluo/r-script
rstats statistical-analysis
Last synced: about 5 hours ago
JSON representation
R Script for research
- Host: GitHub
- URL: https://github.com/czheluo/r-script
- Owner: czheluo
- Created: 2019-04-26T01:48:14.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2024-07-29T01:22:18.000Z (4 months ago)
- Last Synced: 2024-07-29T02:36:49.603Z (4 months ago)
- Topics: rstats, statistical-analysis
- Language: R
- Homepage:
- Size: 12 MB
- Stars: 4
- Watchers: 2
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# R Script for work
### quickly install github R package
>C:\Windows\System32\drivers\etc\hosts
>git config --global http.sslBackend "openssl"
>git config --global http.sslCAInfo C:/Program Files/R/R-3.6.0/library/openssl/cacert.pem
>git config --global http.sslCAInfo /mnt/ilustre/centos7users/dna/.env/lib/R/library/openssl/cacert.pem
### Build R Package
install packages from the github
library("usethis")
git_sitrep() # git situation report
usethis::create_github_token()# open the website and make new token
usethis::edit_r_environ() #可以改变temp的目录，重启就可以更新path
#get tempdir ：
tempdir()
#EDIT：GITHUB_TOKEN="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"
#• Modify '/mnt/ilustre/users/meng.luo/.Renviron'
#• Restart R for changes to take effect
>git config --global user.email "[email protected]"
>git config --global user.name "czheluo"
> conda install R need change the gun++11 to c++11, and need change install pkg-config (conda install )
>conda install -c conda-forge pkg-config
>conda install -c anaconda hdf5
$ ./configure --prefix=/mnt/ilustre/users/meng.luo/project/RNA/ST/R4.3.3
$ make
$ make install
### Miniconda3 install R
##### ADD CONDA-FORGE
$ conda config --add channels conda-forge
$ conda config --set channel_priority strict
##### INSTALL
$ conda search r-base
$ conda create -n R4.2.2
$ conda activate R4.2.2
$ conda install -c conda-forge -r r-base=4.2.2
##### INSTALL PACKAGES
$conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
$conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
$conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
$conda config --set show_channel_urls yes
### host
>reference
Schulze S, Henkel SG, Driesch D, Guthke R, Linde J. Computational prediction of molecular pathogen-host interactions based on dual transcriptome data. Front Microbiol. 2015;6:65. Published 2015 Feb 6. doi:10.3389/fmicb.2015.00065
### Read sequences along the indicated segments of the AB genome. Read counts (in brackets), read length and genomic position are indicated.
### igraph for network from expression data
### Chord Diagram
### barplot
