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bioinformatics-figures

Collection of scripts and examples that will help visualize sequencing data. Most of the scripts are for visualizing sequencing overlaps from ChIP-seq / DNase-seq / FAIRE-seq experiments using venn diagrams

  • [Venn Diagram examples](Venn Diagram examples/) -- Making venn diagrams in R using limma / Vennerable / VennDiagram libraries (input format conversion). These methods are outdated, see UpSetR instead
  • [Entrez IDs for GREAT](Entrez IDs for GREAT/) -- Convert symbols from GREAT's web interface (hg19) into Entrez identifiers as well as detailed install and usage directions
  • makeVenn/makeVenn.R -- will create 2-5 way venn diagrams from GRanges objects using Vennerable library
  • methylcircleplot/methylcircleplot.R -- will create circles that either filled or not filled depending on methylation status
  • igv.R -- R function to take genomic coordinates and get (pre-exisiting) igv session to output snapshots at thoes locations
  • imageplot -- Is a simple example of making a plot in R with colors (corresponding to expression level) example

A tip for others using R or knitR on github: to highlight code in the final markdown document, replace

```R

with

```S