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README.md

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this file contain all kinds of learning materials

(1) git and github

https://happygitwithr.com/rstudio-git-github.html

the commit messages are necessary for commit by default setting, no matter in CLI or in Rstdio if want to commit without messages: git commit -a --allow-empty-message -m '' # https://stackoverflow.com/questions/6218199/git-commit-with-no-commit-message

(2) R for data science / machine learning

(3) mathematics / statistics

(4) Bioinformatics

(5) Biostatistics

R-Bioconductor-Bioinfo-tips

pipe %>%

bioMart MEME HOMER

  1. IRangers
  2. GRangers
  3. Biobase

all GSExxx files can be down loaded with GEO function geoq <- Biobase::getGEO("GSE9514") e <- geo[[1]] # expressionSet exprs(e) pData(geo[[1]]) names(pData(e)) fData(e) names(fData(e)) annotation(e) assay() rowData()

download to current working dir

download.file("http://bowtie-bio.sourceforge.net/recount/ExpressionSets/bottomly_eset.RData", "bottomly_eset.RData")
load("bottomly_eset.RData") or load(url("http://bowtie-bio.sourceforge.net/recount/ExpressionSets/bottomly_eset.RData"))