README.md

In niccw/repeatCraft: Interactive analysis of repeat elements

repeatCraft

repeatCraft is a Shiny application designed to visualise the result from RepeatCraft pipeline. User can run RepeatCraft pipeline through this web application, starting from RepeatMasker GFF, OUT.

In addition to visualise the result of defragmentation from RepeatCraft pipeline , the web application also allow interactive analysis on: 1) Age estimation by repeat class/ family 2) Annotation difference by different tools (currently support LTR_FINER, TEclass, SINE_scan) 3) Structural features of repeat elements (detect and visualise the Open Reading Frames (ORFs)) of specific copy of repeat family

You can also try the web server at http://131.130.65.134:3838/repeatcraft.

Installation

if (!require(remotes)) { install.packages("remotes") }
remotes::install_github("niccw/repeatCraft")

Run repeatCraft from R

repeatcraft::runApp()

Screenshots

It is recommended to chunk your input GFF and OUT files by chromosome if they are larger than 50 mb, repeatCraft would take a long time to process them.

niccw/repeatCraft documentation built on May 27, 2019, 11:50 p.m.