Author Archives: Yixf

About Yixf

世事浮沉如落木，人生聚散似漂萍。
2月 26

[荐]box plots与BoxPlotR

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box plots

BoxPlotR

This application allows users to generate customized box plots in a number of variants based on their data. A data matrix can be uploaded as a file or pasted into the application. Basic box plots are generated based on the data and can be modified to include additional information. Additional features become available when checking that option. Information about sample sizes can be represented by the width of each box where the widths are proportional to the square roots of the number of observations n. Notches can be added to the boxes. These are defined as +/-1.58*IQR/sqrt(n) which gives roughly 95% confidence that two medians are different. It is also possible to define the whiskers based on the ideas of Spear and Tukey. Additional options of data visualization (violin and bean plots) reveal more information about the underlying data distribution. Plots can be labeled, customized (colors, dimensions, orientation) and exported as eps, pdf and svg files.……【阅读全文】

2月 26

[转]RNA测序研究现状与发展

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原文链接

参考文献

RNA-seq is a recent and immensely popular technology for cataloging and comparing gene expression. Two papers from the international RGASP consortium report on large-scale competitions to identify the best algorithms for RNA-seq analysis, with surprising variability in the results.……【阅读全文】

12月 11

《全民目击》观后感

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关于电脑

  • Windows自带的播放器不能用——容易卡。
  • Windows操作系统不能用——毒！毒！毒！
  • XXX安全卫士、杀毒软件不能用——太“智能”。

关于主题

《全民目击》的主题是什么？绝大多数观众都认为影片赞颂了伟大的父爱。但也许并非如此！……【阅读全文】

12月 07

[荐]Intermediate R/Bioconductor for High-Throughput Sequence Analysis

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Intermediate R/Bioconductor for High-Throughput Sequence Analysis introduces users with some R experience to common Bioconductor work flows for sequence analysis. The course involves a combination of presentations and hands-on exercises. Our starting point is BAM files created by aligning short reads to a reference genome. Topics include exploratory analysis (GenomicRanges, Rsamtools); assessing differential expression of known genes (DESeq); detection, calling, and manipulation of variants (VariantTools, VariantAnnotation). We learn how to integrate results with curated gene and genomic annotations (GenomicFeatures), and to visualize results (GViz, ggbio).……【阅读全文】