/rienv

Retained intron environment.

Primary LanguageRMIT LicenseMIT

rienv

Author: Sean Maden

Programmatic setup for retained intron detection tools with conda. This resource currently supports environment setup for the following tools:

Make environments

Run the shell script conda.sh:

sh conda.sh

Alternatively, set up environments from their .yml files, located at ./inst/yml/:

conda env create -f ./inst/yml/env_interest.yml

Tests

Scripts to test environments, especially using any provided vignette examples, are contained at ./inst/test.

Cross-tool tests

The test BAM files provided by the IntEREst package are contained in the folder ./inst/bam. These consist of a small example BAM .bam and BAM index .bai file aligned with hg19. The example BAM data was used to test each of the retained intron tools, where scripts and test results are contained at ./inst/bam/tests/tooltests/.