26

[荐]box plots与BoxPlotR

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】

十二 07

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

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】

09

[荐]Unix and Perl Primer for Biologists

We have written a basic introductory course for biologists to learn the essential aspects of the Perl programming language. This started as a course for grad students at UC Davis, and we then ran it as a one week intensive course for anyone on campus who was interested (sponsored by the UC Davis Genome Center). The feedback from these courses was very positive and so we have decided that we should make it available to anyone who is interested.……【阅读全文】