deseq如何安装linux_deseq/deseq2 - CSDN
  • 安装R包(“RcppArmadillo”)失败,导致依赖该包的DESeq2 无法使用; 首先对gcc,g++升级至4.7, 但依然报错,还是安装不了RcppArmadillo; 报错如下: $ R > source("https://bioconductor.org/biocLite.R"...

    安装R包(“RcppArmadillo”)失败,导致依赖该包的DESeq2 无法使用;

    首先对gcc,g++升级至4.7
    但依然报错,还是安装不了RcppArmadillo;

    报错如下:

    $ R
    
    > source("https://bioconductor.org/biocLite.R")
    > biocLite("DESeq2")
    BioC_mirror: https://bioconductor.org
    Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.4.1 (2017-06-30).
    Installing package(s) ‘DESeq2’
    also installing the dependencies ‘RcppArmadillo’, ‘locfit’, ‘geneplotter’
    
    trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/RcppArmadillo_0.7.960.1.1.tar.gz'
    Content type 'application/octet-stream' length 1115539 bytes (1.1 MB)
    ==================================================
    downloaded 1.1 MB
    
    trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/locfit_1.5-9.1.tar.gz'
    Content type 'application/octet-stream' length 196560 bytes (191 KB)
    ==================================================
    downloaded 191 KB
    
    trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/geneplotter_1.48.0.tar.gz'
    Content type 'application/x-gzip' length 1400072 bytes (1.3 MB)
    ==================================================
    downloaded 1.3 MB
    
    trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/DESeq2_1.10.1.tar.gz'
    Content type 'application/x-gzip' length 1255971 bytes (1.2 MB)
    ==================================================
    downloaded 1.2 MB
    
    * installing *source* package ‘RcppArmadillo’ ...
    ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
    checking whether the C++ compiler works... yes
    checking for C++ compiler default output file name... a.out
    checking for suffix of executables... 
    checking whether we are cross compiling... no
    checking for suffix of object files... o
    checking whether we are using the GNU C++ compiler... yes
    checking whether g++ -m64 accepts -g... yes
    checking how to run the C++ preprocessor... g++ -m64 -E
    checking whether we are using the GNU C++ compiler... (cached) yes
    checking whether g++ -m64 accepts -g... (cached) yes
    checking whether g++ version is sufficient... no
    configure: WARNING: Only g++ version 4.7.2 or greater can be used with RcppArmadillo.
    configure: error: Please use a different compiler.
    ERROR: configuration failed for package ‘RcppArmadillo’
    * removing ‘/public/home/user/R/x86_64-redhat-linux-gnu-library/3.4/RcppArmadillo’
    * installing *source* package ‘locfit’ ...
    ** package ‘locfit’ successfully unpacked and MD5 sums checked
    ** libs
    gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG   -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC   -c S_enter.c -o S_enter.o
    ......
    gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG   -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -
    gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -o locfit.so S_enter.o band.o dbinom.o dens_haz.o dens_int.o dens_odi.o density.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_sphere.o ev_trian.o family.o fitted.o frend.o lf_adap.o lf_dercor.o lf_fitfun.o lf_nbhd.o lf_robust.o lf_vari.o lf_wdiag.o lfstr.o locfit.o m_chol.o m_eigen.o m_icirc.o m_imont.o m_isimp.o m_isphr.o m_jacob.o m_max.o m_qr.o m_solve.o m_svd.o m_vector.o math.o minmax.o pcomp.o preplot.o prob.o procv.o scb.o scb_cons.o scb_crit.o scb_iface.o simul.o smisc.o startlf.o weight.o -L/usr/lib64/R/lib -lR
    installing to /public/home/user/R/x86_64-redhat-linux-gnu-library/3.4/locfit/libs
    ** R
    ** data
    ** preparing package for lazy loading
    ** help
    *** installing help indices
     .........
    ** building package indices
    ** testing if installed package can be loaded
    * DONE (locfit)
    * installing *source* package ‘geneplotter’ ...
    ** R
    ** data
    ** inst
    ** preparing package for lazy loading
    ** help
    *** installing help indices
      ......
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded
    * DONE (geneplotter)
    ERROR: dependency ‘RcppArmadillo’ is not available for package ‘DESeq2’
    * removing ‘/public/home/user/R/x86_64-redhat-linux-gnu-library/3.4/DESeq2’
    
    
    
    $ gcc --version
    gcc (GCC) 4.7.2 20121015 (Red Hat 4.7.2-5)
    Copyright (C) 2012 Free Software Foundation, Inc.
    This is free software; see the source for copying conditions.  There is NO
    warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

    解决方法:

    ## R version 3.4.1 (2017-06-30)
    ## Platform: x86_64-redhat-linux-gnu (64-bit)
    ## Running under: CentOS release 6.5 (Final)
    #安装低版本的RcppArmadillo包
    #Old sources---RcppArmadillo archive: https://cran.r-project.org/src/contrib/Archive/RcppArmadillo/
    install.packages("https://cran.r-project.org/src/contrib/Archive/RcppArmadillo/RcppArmadillo_0.3.930.1.tar.gz", repos=NULL)
    
    source("https://bioconductor.org/biocLite.R")
    biocLite("DESeq2")
    

    MADE IT ^ _^

    转载于:https://www.cnblogs.com/adawong/p/7429910.html

    展开全文
  • DESeq2 install 如何安装R包 RcppArmadillo

    万次阅读 2020-06-08 15:52:41
    安装R包( ‘RcppArmadillo’)失败,导致依赖该包的DESeq2 无法使用;首先对gcc,g++升级至4.7, 但依然报错,还是安装不了RcppArmadillo;报错如下:$ R> source("https://bioconductor.org/biocLite.R") ...

    安装R包(“RcppArmadillo”)失败,导致依赖该包的DESeq2 无法使用;

    首先对gcc,g++升级至4.7
    但依然报错,还是安装不了RcppArmadillo;

    报错如下:

    $ R
    
    > source("https://bioconductor.org/biocLite.R")
    > biocLite("DESeq2")
    BioC_mirror: https://bioconductor.org
    Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.4.1 (2017-06-30).
    Installing package(s) ‘DESeq2’
    also installing the dependencies ‘RcppArmadillo’, ‘locfit’, ‘geneplotter’
    
    trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/RcppArmadillo_0.7.960.1.1.tar.gz'
    Content type 'application/octet-stream' length 1115539 bytes (1.1 MB)
    ==================================================
    downloaded 1.1 MB
    
    trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/locfit_1.5-9.1.tar.gz'
    Content type 'application/octet-stream' length 196560 bytes (191 KB)
    ==================================================
    downloaded 191 KB
    
    trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/geneplotter_1.48.0.tar.gz'
    Content type 'application/x-gzip' length 1400072 bytes (1.3 MB)
    ==================================================
    downloaded 1.3 MB
    
    trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/DESeq2_1.10.1.tar.gz'
    Content type 'application/x-gzip' length 1255971 bytes (1.2 MB)
    ==================================================
    downloaded 1.2 MB
    
    * installing *source* package ‘RcppArmadillo’ ...
    ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
    checking whether the C++ compiler works... yes
    checking for C++ compiler default output file name... a.out
    checking for suffix of executables... 
    checking whether we are cross compiling... no
    checking for suffix of object files... o
    checking whether we are using the GNU C++ compiler... yes
    checking whether g++ -m64 accepts -g... yes
    checking how to run the C++ preprocessor... g++ -m64 -E
    checking whether we are using the GNU C++ compiler... (cached) yes
    checking whether g++ -m64 accepts -g... (cached) yes
    checking whether g++ version is sufficient... no
    configure: WARNING: Only g++ version 4.7.2 or greater can be used with RcppArmadillo.
    configure: error: Please use a different compiler.
    ERROR: configuration failed for package ‘RcppArmadillo’
    * removing ‘/public/home/user/R/x86_64-redhat-linux-gnu-library/3.4/RcppArmadillo’
    * installing *source* package ‘locfit’ ...
    ** package ‘locfit’ successfully unpacked and MD5 sums checked
    ** libs
    gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG   -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC   -c S_enter.c -o S_enter.o
    ......
    gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG   -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -
    gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -o locfit.so S_enter.o band.o dbinom.o dens_haz.o dens_int.o dens_odi.o density.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_sphere.o ev_trian.o family.o fitted.o frend.o lf_adap.o lf_dercor.o lf_fitfun.o lf_nbhd.o lf_robust.o lf_vari.o lf_wdiag.o lfstr.o locfit.o m_chol.o m_eigen.o m_icirc.o m_imont.o m_isimp.o m_isphr.o m_jacob.o m_max.o m_qr.o m_solve.o m_svd.o m_vector.o math.o minmax.o pcomp.o preplot.o prob.o procv.o scb.o scb_cons.o scb_crit.o scb_iface.o simul.o smisc.o startlf.o weight.o -L/usr/lib64/R/lib -lR
    installing to /public/home/user/R/x86_64-redhat-linux-gnu-library/3.4/locfit/libs
    ** R
    ** data
    ** preparing package for lazy loading
    ** help
    *** installing help indices
     .........
    ** building package indices
    ** testing if installed package can be loaded
    * DONE (locfit)
    * installing *source* package ‘geneplotter’ ...
    ** R
    ** data
    ** inst
    ** preparing package for lazy loading
    ** help
    *** installing help indices
      ......
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded
    * DONE (geneplotter)
    ERROR: dependency ‘RcppArmadillo’ is not available for package ‘DESeq2’
    * removing ‘/public/home/user/R/x86_64-redhat-linux-gnu-library/3.4/DESeq2’
    
    
    
    $ gcc --version
    gcc (GCC) 4.7.2 20121015 (Red Hat 4.7.2-5)
    Copyright (C) 2012 Free Software Foundation, Inc.
    This is free software; see the source for copying conditions.  There is NO
    warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
    

    解决方法:

    ## R version 3.4.1 (2017-06-30)
    ## Platform: x86_64-redhat-linux-gnu (64-bit)
    ## Running under: CentOS release 6.5 (Final)
    #安装低版本的RcppArmadillo包
    #Old sources---RcppArmadillo archive: https://cran.r-project.org/src/contrib/Archive/RcppArmadillo/
    install.packages("https://cran.r-project.org/src/contrib/Archive/RcppArmadillo/RcppArmadillo_0.3.930.1.tar.gz", repos=NULL)
    # or
    wget -c https://cran.r-project.org/src/contrib/Archive/RcppArmadillo/RcppArmadillo_0.3.930.1.tar.gz
    R CMD INSTALL -l /home/your_username/R_libs RcppArmadillo_0.3.930.1.tar.gz
    
    source("https://bioconductor.org/biocLite.R")
    biocLite("DESeq2")
    
    
    
    

    MADE IT ^ _^

    展开全文
  • DESeq采用NB(负二项分布检验的方式)对reads数进行差异显著性检验,同时还增加了矫正由于长度引起的误差,估算基因表达量的方式采用basemean值来估算表达量(标准化以后)这里,我在R下安装DESeq包出现了一些问题...

    DESeq采用NB(负二项分布检验的方式)对reads数进行差异显著性检验,同时还增加了矫正由于长度引起的误差,估算基因表达量的方式采用basemean值来估算表达量(标准化以后)这里,我在R下安装DESeq包出现了一些问题帮助总结一下。

    首先,我的R是15.0版本

    打开R
    source("http://bioconductor.org/biocLite.R")
    biocLite(‘DEseq’)
    会出现安装成功
    loading的时候缺少locfit包则需要再输入(locfit包只在15.1版本下编译的,不过貌似没什么问题)
    biocLite(‘locfit’)
    再loading会出现缺少xtable包
    输入
    biocLite(‘xtable’)
    在loading会出现XML报错
    输入
    biocLite(‘XML’)
    这样DESeq就运行没有问题了。

    注中间可能会出现某个包无法安装的情况,注意检查网络连接


    下面具体的如何进行差异显著性检验,我参考别人的数据,这里计算出reads在每个样本中各个基因上的counts数文件,下面couns_...分别表示6个样本(三个重复对照三个重复处理组)

             library(DESeq)

            setwd("wherethe data is")

            #设置工作路径,可以再GUI上面直接设置

            c1<-read.table("counts_074284",row.names=1)

            c2<-read.table("counts_074286",row.names=1)

            c3<-read.table("counts_074262",row.names=1)

            c4<-read.table("counts_074263",row.names=1)

            c5<-read.table("counts_074264",row.names=1)

            c6<-read.table("counts_074285",row.names=1)

            #读入几组counts数据

            counts<-cbind(c1,c2,c3,c4,c5,c6)

            counts<-counts[-c(32679:32683),]  #remove the more general lines

            colnames(counts)<-c("P1","P2","P3","M1","M2","M3")

            #讲数据放到表中

            design<- rep (c("P","Mo"),each=3)

            #描述实验设置重复

              de  <- newCountDataSet(counts, design)

            #de  <- estimateSizeFactors(de)

            de  <-  estimateDispersions(de)

            de<- estimateDispersions(de)

            res  <- nbinomTest(de,"P","Mo")

            #计算结果

             sum(na.omit(res$padj<0.05))

            #输出差异显著的值。
    #最后再加一部把数据输出出来,这个我就不用说了
        write.table(res,file="file.csv",sep=",")
    

    展开全文
  • #运行时间明显缩短了,尤其在样本数据多时非常明显。

    在这里插入图片描述
    #运行时间明显缩短了,尤其在样本数据多时非常明显。

    展开全文
  • DESeq2差异基因分析和批次效应移除

    万次阅读 2018-07-26 15:40:35
    差异基因鉴定 基因表达标准化 不同样品的测序量会有差异,最简单的标准化方式是计算 counts per million (CPM),即原始reads count除以总reads数乘以1,000,000。 这种计算方式的缺点是容易受到极高表达且在...
  • 安装 R package的2种方法

    千次阅读 2016-02-23 15:43:37
    安装R package的2种方法 安装R语言的包的方法: 1. 自动安装(在线安装) 在R的控制台,输入 install.packages(“stepNorm”,contriburl=”http://www.your.url”, dependencies = TRUE) 若要...
  • featureCounts的使用featureCounts的安装featureCounts的使用 featureCounts的安装 在转录组进行统计基因count数的时候,Htseq-count与featureCounts为使用最多的软件,其中htseq-count的速度较慢,而featureCounts...
  • 利用R包DEseq2进行差异表达分析和可视化 count数矩阵 在Linux下,通过HISAT2 对下载的GSE数据进行比对,FeatureCounts软件进行基因水平定量,得到count数矩阵。之后便可以载入R语言中进行差异分析。 差异分析 第...
  • Trinity的安装与使用

    千次阅读 2018-10-23 21:04:05
    Trinity是由 Broad Institute开发的,用于转录本的de novo拼接,主要由三个软件模块组成:Inchworm, Chrysalis and Butterfly,能处理大型的RNA数据。 ...Trinity partitions the sequence data into...
  • HISAT2+StringTie+Ballgown安装及使用流程 2015年Nature Methods上面发表了一款快速比对工具hisat,作为接替tophat和bowtie的比对工具,它具有更快的比对速度和更高的比对率,最近把这个流程走完一遍,感觉优势还是...
  • ​ LAMP搭建的网站在ubuntu14.04,有用户文件上传和下载,后台程序以R脚本运行为主,本机安装的R为3.4.4,需要安装最新3.6 搭配最新的R包。本来想着用conda来安装,但是 apahce无法找到R执行文件,因此还得重新全局...
  • installation of package xx had non-zero exit status 在安装包时如遇到非零错误: 手动在CRAN下载包,注意依赖,CRAN页面中以import:xxx标出 install.packages("~/Downloads/MathiasHarrer-dmetar-17a76a3.tar.gz...
  • Cufflinks的使用

    万次阅读 2015-04-01 21:52:50
    一. 简介 Cufflinks下主要包含cufflinks,cuffmerge,cuffcompare和cuffdiff等几支主要的程序。...1. 为了安装Cufflinks,必须有Boost C++ libraries。下载Boost并安装。默认安装在/usr/local。 $ tar jxvf bo
  • 因为我的服务器没有外网的原因,尝试了对R设置清华镜像源,可以下载R相关的包,但生物信息学分析会用到很多Bioconductor的软件,需要使用BiocManager软件,试了几次发现服务器中无法安装BiocManager软件,或者使用...
  • 1.关于准备工作 2. 3.FastQC流程代码 4.Hisat2流程代码 #! /bin/bash #上面一行宣告这个script的语法使用bash语法,当程序被执行时,能够载入bash的相关环境配置文件。 # Program: # This program is used for ...
  • .libPaths("~/R/x86_64-pc-linux-gnu-library/2.11") print(.libPaths()) print(sessionInfo()) print(version) </code></pre> <p>And the output before the error confirms that I am indeed running R 2.14.2 ...
  • R语言绘图实战(myteacher:ZJU陈铭老师。所有的内容均来自对陈老师上课的整理) R是用于统计分析、绘图的语言和操作环境,是一门用于统计计算和作图的解释性语言,受S语言和Scheme语言影响发展...LINUX WINDOWS MA...
  • istream, outstream使用及常见错误

    万次阅读 2015-01-04 10:27:16
    如下面的例子中,实现读取并处理deseq文件夹下所有文件,输出到ostream fw.code:头文件:#include #include #include #include #include #include调用:void process(char* filename){ std::filebuf fbOut,
  • 欢迎订阅WX众号:基因学苑,更多精彩内容等你发掘! 基因学苑Q群:32798724 编者按 虽然短序列比对工具subread的使用没有bwa和hisat2流行,但是软件包中的featureCounts工具却使用比较广泛。尤其是在利用R语言进行...
  • 同济GFOLD软件是一款根据mapping结果直接进行差异表达分析的软件,http://www.tongji.edu.cn/~zhanglab/GFOLD/index.html,文献中提到,该软件在分析无重复的转录组...结果要优于其他DESeq、edgeR、cuffldiff等软件,故
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