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=head2 testsimsGSL.R

This script is used to test the performance of the GSL RNGs against the 
inverse CDF implemented via a procedural logic in R. It outputs a single
PNG file with the violin plots (a combination of box plots and kernel density)
of the timing data for different possible implementations of the inverse CDF
method in either R or Perl.

=head2 vioplot_Perl_R_lognormal.png

Performance comparison of Perl and R for the generation of truncated lognormal
variates. It is produced by testsimsGSL.R

=head2 testPerl.csv

This is a CSV file that contains the timing data for the Perl RNGs and the
inverse CDF method implemented in PDL. It is produced by testRNG_performance.pl

=head2 perl_timing.txt

This is a text file that contains the timing data for the various implementations
of cutadapt in native Perl, PDL and PDL/C methods. It is produced by the script
cutadapt_polyA_algo_timing.pl

=head2 python_timing.txt

This is a text file that contains the timing data for the various implementations
of cutadapt in native Python. It is produced by the script cutadapt_polyA_algo_timing.py


=head1 SEE ALSO

=over 4


=item * L<Bio::SeqAlignment|https://metacpan.org/pod/Bio::SeqAlignment>

A collection of tools and libraries for aligning biological sequences 
from within Perl. 

=item * L<cutadapt|https://metacpan.org/pod/Bio::SeqAlignment::cutadapt>

This module provides an interface to the cutadapt tool for identifying and
trimming adapters and primers from sequencing data.


=item * L<PDL|https://metacpan.org/pod/PDL>

The Perl Data Language (PDL) gives standard Perl the ability to compactly store
and speedily manipulate the large N-dimensional data arrays which are the bread
and butter of scientific computing. PDL turns Perl into a free, array-oriented,
numerical language that can be a very solid alternative to switching to Python
or R for numerical computations during complex data analysis tasks and 
pipelines. 

=item * L<polyester|https://github.com/alyssafrazee/polyester>

Polyester is an R package designed to simulate RNA sequencing experiments with
differential transcript expression.Given a set of annotated transcripts, 
Polyester will simulate the steps of an RNA-seq experiment (fragmentation, 
reverse-complementing, and sequencing) and produce files containing simulated 
RNA-seq reads. Simulated reads can be analyzed using your choice of downstream 
analysis tools.
Polyester has a built-in wrapper function to simulate a case/control experiment 
with differential transcript expression and biological replicates. Users are 
able to set the levels of differential expression at transcripts of their 
choosing. This means they know which transcripts are differentially expressed 
in the simulated dataset, so accuracy of statistical methods for differential 
expression detection can be analyzed.

=back

=head1 AUTHOR

Christos Argyropoulos <chrisarg@cpan.org>

=head1 COPYRIGHT AND LICENSE

This software is copyright (c) 2024 by Christos Argyropoulos.

This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.

=cut