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[…] > protein_data_B30_min<-protein_data[1:2548,10:12] > protein_data_M30_min<-protein_data[1:2548,19:21] > protein_data_30_min<-data.frame(protein_data_B30_min,protein_data_M30_min) > protein_data_30_min[1:2,] B30 B30.1 B30.2 Mgo30 Mgo30.1 Mgo30.2 1 870.5042 867.0873 0 1086.82[......] […] Summary: Counting all the k-mers (substrings of length k) in DNA/RNA sequencing reads is the preliminary step of many bioinformatics applications. However, state of the art k-mer counting methods require that a large data structure resides in memory. Such structure typically grows with the number of[……] […] http://www.afreevpn.com/ www.bestfreevpn.com […] Circos: nucmer –prefix=refBAV1_qryVScds Dehalococcoides_BAV1.fasta Dehalococcoides_VS.cds.fasta show-tiling -i 80 -c refBAV1_qryVScds.delta > refBAV1_qryVScds.tiling awk -F ” ” ‘{print “chr1″ “\t” $1 “\t” $2}’ refBAV1_qryVScds.tiling > Dehalococcoidessp.VScds.gene_tableBAV1.txt shenzy@s[……] […] Codon adaptation index (CAI) is one of them. To examine the CAI value of a gene, a reference table of RSCU (relative synonymous codon usage) values for highly expressed genes is compiled. A software call CodonW, you can download it from: http://codonw.sourceforge.net/. There is also a PhD thesis[……] […] 今天一个同学给我推荐一篇Nature Protocol 上文章，关于转录组差异表达分析。尚在正式通读之前习惯性浏览一遍图表，说实在这篇文章着实让我觉得有点“另类”。这是一篇活生生的利用Bowtie、tophat和Cufflinks做转录组差异表达分析的protocol。里面详细讲解每一步需要分析什么，用哪些些软件，已经相关命令和参数。 根据文章介绍的workflow，做转录组分析，无论是链特异性转录组数据（Strand-specific RNA-seq）还是非特异性数据，主要内容包括下面几个部分： 1）reads mapping，这里面推荐两款软件一个是Bowtie，另一个是top[……] […]
> install.packages('plotrix') Installing package(s) into ‘/home/shenzy/R/x86_64-pc-linux-gnu-library/2.15’ (as ‘lib’ is unspecified) 试开URL’http://cran.csiro.au/src/contrib/plotrix_3.4-5.tar.gz' Content type 'application/x-gzip' length 211113 bytes (206 Kb) 打开了URL ==================[......]
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