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more_vis_analysis.md

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Downstream analysis of vector integration sites

Inputs

The main input is a tab-separated file generated by the qsLAM pipeline expalined in this repository. An example of input file: picture2

Usages

A few files are included:

  • hg19.basic.annotation.update.Rdata (a dataframe of hg19 annotation in R format)
  • LVIS_functions.R (a list of functions called by other analysis scripts)
  • compile_VIS.R (a tutorial showing how to take the inputs and perform VIS integration across samples)
  • vis_visualization_examples.R (a tutorial showing how to use some of the visualization functions)
  • all_P4_collect_IS.Rdata (an example: vis outputed from the qsLAM pipeline for a patient)