Kwalitee Issues

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Add =head1 LICENSE and the text of the license to the main module in your code.

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Add =head1 LICENSE and/or the proper text of the well-known license to the main module in your code.

meta_yml_declares_perl_version

If you are using Build.PL define the {requires}{perl} = VERSION field. If you are using MakeMaker (Makefile.PL) you should upgrade ExtUtils::MakeMaker to 6.48 and use MIN_PERL_VERSION parameter. Perl::MinimumVersion can help you determine which version of Perl your module needs.

meta_yml_has_provides

Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.

Modules

Name Abstract Version View
CLIPSeqTools A collection of tools for the analysis of CLIP-Seq data. 0.001008 metacpan
CLIPSeqTools::App Main CLIPSeqTools application with tools for analysis of CLIP-Seq libraries. 0.001008 metacpan
CLIPSeqTools::App::all Run all clipseqtools analyses 0.001008 metacpan
CLIPSeqTools::App::cluster_size_and_score_distribution Assemble reads in clusters and measure their size and number of contained reads distribution 0.001008 metacpan
CLIPSeqTools::App::conservation_distribution Measure reads at each conservation level 0.001008 metacpan
CLIPSeqTools::App::count_reads_on_genic_elements Count reads on transcripts, genes, exons, introns 0.001008 metacpan
CLIPSeqTools::App::distribution_on_genic_elements Measure read distribution on 5'UTR, CDS and 3'UTR. 0.001008 metacpan
CLIPSeqTools::App::distribution_on_introns_exons Measure read distribution on exons and introns. 0.001008 metacpan
CLIPSeqTools::App::export_bed Export reads to a BED file. 0.001008 metacpan
CLIPSeqTools::App::genome_coverage Measure percent of genome covered by reads. 0.001008 metacpan
CLIPSeqTools::App::genomic_distribution Count reads on genes, repeats, exons, introns, 5'UTRs, ... 0.001008 metacpan
CLIPSeqTools::App::nmer_enrichment_over_shuffled Measure Nmer enrichment over shuffled reads. 0.001008 metacpan
CLIPSeqTools::App::nucleotide_composition Measure nucleotide composition along reads. 0.001008 metacpan
CLIPSeqTools::App::reads_long_gaps_size_distribution Measure size distribution of long alignment gaps produced by a gap aware aligner. 0.001008 metacpan
CLIPSeqTools::App::size_distribution Measure size distribution for reads. 0.001008 metacpan
CLIPSeqTools::CompareApp A collection of tools to compare two CLIP-Seq libraries. 0.001008 metacpan
CLIPSeqTools::CompareApp::all Run all clipseqtools-compare analyses. 0.001008 metacpan
CLIPSeqTools::CompareApp::compare_counts Compare tables with counts. 0.001008 metacpan
CLIPSeqTools::CompareApp::join_tables Perform inner join on tab delimited table files. Can be used to prepare DESeq input file from counts tables. 0.001008 metacpan
CLIPSeqTools::CompareApp::libraries_overlap_stats Count reads of library A that overlap reads in reference library B. 0.001008 metacpan
CLIPSeqTools::CompareApp::libraries_relative_read_density Measure read density around the reads of a reference library 0.001008 metacpan
CLIPSeqTools::PlotApp Tools to create plots based on the output of CLIPSeqTools applications. 0.001008 metacpan
CLIPSeqTools::PlotApp::cluster_size_and_score_distribution Create plots for script cluster_size_and_score_distribution. 0.001008 metacpan
CLIPSeqTools::PlotApp::conservation_distribution Create plots for script conservation_distribution. 0.001008 metacpan
CLIPSeqTools::PlotApp::distribution_on_genic_elements Create plots for script distribution_on_genic_elements. 0.001008 metacpan
CLIPSeqTools::PlotApp::distribution_on_introns_exons Create plots for script distribution_on_introns_exons. 0.001008 metacpan
CLIPSeqTools::PlotApp::genomic_distribution Create plots for script genomic_distribution. 0.001008 metacpan
CLIPSeqTools::PlotApp::libraries_relative_read_density Create plots for script libraries_relative_read_density. 0.001008 metacpan
CLIPSeqTools::PlotApp::nucleotide_composition Create plots for script nucleotide_composition. 0.001008 metacpan
CLIPSeqTools::PlotApp::reads_long_gaps_size_distribution Create plots for script reads_long_gaps_size_distribution. 0.001008 metacpan
CLIPSeqTools::PlotApp::scatterplot Create scatterplot for two tables. 0.001008 metacpan
CLIPSeqTools::PlotApp::size_distribution Create plots for script size_distribution. 0.001008 metacpan
CLIPSeqTools::PreprocessApp Tools to process a fastq file with CLIP-Seq data into a database compatible with clipseqtools. 0.001008 metacpan
CLIPSeqTools::PreprocessApp::all Run all clipseqtools-preprocess analyses. 0.001008 metacpan
CLIPSeqTools::PreprocessApp::annotate_with_conservation Annotate alignments in a database table with conservation scores. 0.001008 metacpan
CLIPSeqTools::PreprocessApp::annotate_with_deletions Annotate alignments in a database table with deletions. 0.001008 metacpan
CLIPSeqTools::PreprocessApp::annotate_with_file Annotate alignments in a database table with regions from a BED/SAM file. 0.001008 metacpan
CLIPSeqTools::PreprocessApp::annotate_with_genic_elements Annotate alignments in a database table with genic information. 0.001008 metacpan
CLIPSeqTools::PreprocessApp::cleanup_alignment Keep a single record for multimappers, sort and collapse similar STAR alignments. 0.001008 metacpan
CLIPSeqTools::PreprocessApp::collapse_fastq Keep a single record for identical sequences 0.001008 metacpan
CLIPSeqTools::PreprocessApp::cut_adaptor Cut the adaptor sequence from the 3'end of reads. 0.001008 metacpan
CLIPSeqTools::PreprocessApp::sam_to_sqlite Load a SAM file in an SQLite database. 0.001008 metacpan
CLIPSeqTools::PreprocessApp::star_alignment Do reads alignment with STAR. 0.001008 metacpan
CLIPSeqTools::PreprocessApp::trim_fastq Trim N nucleotides from the start and/or end of FASTQ sequences. 0.001008 metacpan
CLIPSeqTools::Role::Option::Genes Role to enable reading a GTF file with genes/transcripts from the command line 0.001008 metacpan
CLIPSeqTools::Role::Option::Library Role to enable reading a library with reads from the command line 0.001008 metacpan
CLIPSeqTools::Role::Option::OutputPrefix Role to enable output prefix as command line option. 0.001008 metacpan
CLIPSeqTools::Role::Option::Plot Role to enable plot as command line option 0.001008 metacpan
CLIPSeqTools::Role::Option::ReferenceLibrary Role to enable reading reference libraries with reads from the command line 0.001008 metacpan
CLIPSeqTools::Role::Option::Transcripts Role to enable reading a GTF file with transcripts from the command line 0.001008 metacpan

Other Files

MANIFEST metacpan
META.json metacpan
META.yml metacpan
Makefile.PL metacpan
README.md metacpan
dist.ini metacpan