txdb初识 谈到txdb,我们不得不提两个包,'GenomicFeatures'和“Txdb.Hsapiens.UCSC.hg38.knownGene”,这两个包都是用来创建Txdb对象。当然有的人用的是hg19,我这里采用最新的hg38,操作函数都是一样的,只是所包含的信息更多。 使用R加载两个包 首先,我们先把这两个包安装起来,接下来一步步来看Txdb究竟是什么东西 ...
[Bioc-devel] A bug in TxDb.Hsapiens.UCSC.hg38.knownGene? = 2.14.0), ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene,FunciSNP.data]]>plyr, org.Hs.eg.db, snpStats, ggplot2 (>= 0.9.0), reshape (> = 0.8.4), scales Enhances parallel Description FunciSNP integrates information from GWAS, 1000...
Installing package(s) ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ installing the source package ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz' Content type 'application/x-gzip' length ...
成功解决,安装 XML 时同样也是这个问题 ,跟上面是一种解决方式 问题2 用BiocManager 下载TxDb.Hsapiens.UCSC.hg38.knownGen报错 主要问题是包比较老,尝试用 biocLite 解决 >source("https://bioconductor.org/biocLite.R") >biocLite("TxDb.Hsapiens.UCSC.hg38.knownGen") BioC_mirror: https://bioconductor.org ...
("TxDb.Hsapiens.UCSC.hg38.knownGene")>hg38.refseq.db=TxDb.Hsapiens.UCSC.hg38.knownGene>hg38.refseq.db TxDb object:# Db type: TxDb# Supporting package: GenomicFeatures# Data source: UCSC# Genome: hg38# Organism: Homo sapiens# Taxonomy ID: 9606# UCSC Table: knownGene# UCSC Track: GENCODE...