The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Chromatra T

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CHROMATRA T visualizes the enrichment of chromatin modification across genomic features in an unbiased way by accounting for feature length and further grouping features based on a second characteristic (e.g. transcriptional frequency of transcripts).

Quick Start

Test Data

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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> chromatrat.

Input File(s)

Use H2AZ_WT_AllData_sample.gff3 and sample_transcripts_for_Chromatra_T.tsv  from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Default parameters only, no further configuration needed.

Output File(s)

Expect an image as output. For the test case, the output file you will find in the example_data directory is named test.png.

Tool Source for App

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