科学网—Kevin2015的留言板

IP: 14.204.63.* [8]张洪磊 2016-5-24 09:27

http://www.bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html

IP: 14.204.63.* [7]张洪磊 2016-5-19 10:44

biocLite("GenomicFeatures")
biocLite("TxDb.Hsapiens.UCSC.hg38.knownGene")
biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")
biocLite("TxDb.Mmusculus.UCSC.mm10.knownGene")
biocLite("TxDb.Mmusculus.UCSC.mm9.knownGene")
biocLite("org.Mm.eg.db")
biocLite("org.Hs.eg.db")

IP: 14.204.63.* [6]张洪磊 2016-5-18 23:03

genomic features
http://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html

IP: 14.204.63.* [5]张洪磊 2016-5-18 15:19

library(edgeR)
x <- read.csv("313Rvs403R.csv",row.names="Gene")
group<-factor(c(1,2))
y <- DGEList(counts=x,group=group)
keep <- rowSums(cpm(y) > 1) >= 1
y<-y[keep,]
dim(y)
y <- calcNormFactors(y)
y <- estimateGLMCommonDisp(y,method="deviance", robust="TRUE",subset=NULL)
et <- exactTest(y)
de<-topTags(et,n=20000)
write.table(de, file = "313Rvs403Rdiff.txt", row.names = T, quote = F)

IP: 14.204.63.* [4]张洪磊 2016-5-18 10:51

python自学推荐廖雪峰的博客http://www.liaoxuefeng.com/wiki/0014316089557264a6b348958f449949df42a6d3a2e542c000

IP: 14.204.63.* [3]张洪磊 2016-5-17 11:31

ChIPseeker: an R package for ChIP peak Annotation, Comparison and Visualization
http://www.bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html

IP: 14.204.63.* [2]张洪磊 2016-5-17 11:00

gsea (生信菜鸟团链接): http://www.bio-info-trainee.com/1334.html

IP: 14.204.63.* [1]张洪磊 2016-5-11 17:05

gene_information: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/

Kevin2015的个人博客分享 http://blog.sciencenet.cn/u/Kevin2015

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