In qenvio/hicvidere:

hicvidere

hicvidere is a minimal package to ease in the visualization of HiC data (contact maps). It is based on fast data retrieval provided by tabix via seqminer.

Quick start

You can install the package from github

devtools::install_github("qenvio/hicvidere")

To start a interactive shiny app that wraps the main functionalities of the package just code

library("hicvidere")
runSimple()

The app will ask you to select a headless *.TSV (tab separated values) file with the information of the samples/experiments. The first two fields/columns are mandatory:

1. unique name to identify each sample/experiment.

2. path to the compressed and indexed file of contacts. Both local and remote (via URI) data retrieval are supported. More about the required format in the file format section.

File format

hicvidere requires the contact matrix information in a bed-like format. These are the mandatory fields/columns:

1. chromosome

2. genomic location of the row bin

3. genomic location of the column bin

4. number of contacts between row and column bins

hicvidere only needs the upper triangular contact matrix (so row position >= column position).

This bed-like file should be sorted, compressed and indexed. See tabix documentation.

qenvio/hicvidere documentation built on May 26, 2019, 11:35 a.m.