Cytoscape基础教程笔记

昨天开始学用Cytoscape,其tutorial分为两个部分,基础的和高级的。基础教程又分成了四课:Getting Started、Filters & Editor、Fetching External Data和Expression Analysis。为防忘记,做个摘记。

第一课 新手上路,地址见http://goo.gl/FJLxp。 Cytoscape可以本地安装,也可以web start。软件得用java,所以要装JRE。我在Ubuntu下装了OpenJDK,可以运行。因为以前一直没把jnlp文件和java关联起来,所以从没成功web start过,试了一下“课文”[……]

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Reading the NCBI’s GEO microarray SOFT files in R/BioConductor

http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/geo/ This page discusses how to load GEO SOFT format microarray data from the Gene Expression Omnibus database (GEO) (hosted by the NCBI) into R/BioConductor. SOFT stands for Simple Omnibus Format in Text. There are actually four[……]

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RSeQC: quality control of RNA-seq experiments

Abstract

Motivation: RNA-seq has been extensively used for transcriptome study. Quality control (QC) is critical to ensure that RNA-seq data are of high quality and suitable for subsequent analyses. However, QC is a time-consuming and complex task, due to the massive size and versatile nature of RN[……]

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