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Emmanouil "Manolis" Maragkakis > CLIPSeqTools


This Release CLIPSeqTools-0.1.8  [Download] [Browse 17 May 2018
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License The Perl 5 License (Artistic 1 & GPL 1)
Special Files


CLIPSeqTools A collection of tools for the analysis of CLIP-Seq data.     0.1.8
CLIPSeqTools::App Main CLIPSeqTools application with tools for analysis of CLIP-Seq libraries.     0.1.8
CLIPSeqTools::App::all Run all clipseqtools analyses     0.1.8
CLIPSeqTools::App::cluster_size_and_score_distribution Assemble reads in clusters and measure their size and number of contained reads distribution     0.1.8
CLIPSeqTools::App::conservation_distribution Measure reads at each conservation level     0.1.8
CLIPSeqTools::App::count_reads_on_genic_elements Count reads on transcripts, genes, exons, introns     0.1.8
CLIPSeqTools::App::distribution_on_genic_elements Measure read distribution on 5'UTR, CDS and 3'UTR.     0.1.8
CLIPSeqTools::App::distribution_on_introns_exons Measure read distribution on exons and introns.     0.1.8
CLIPSeqTools::App::export_bed Export reads to a BED file.     0.1.8
CLIPSeqTools::App::genome_coverage Measure percent of genome covered by reads.     0.1.8
CLIPSeqTools::App::genomic_distribution Count reads on genes, repeats, exons, introns, 5'UTRs, ...     0.1.8
CLIPSeqTools::App::nmer_enrichment_over_shuffled Measure Nmer enrichment over shuffled reads.     0.1.8
CLIPSeqTools::App::nucleotide_composition Measure nucleotide composition along reads.     0.1.8
CLIPSeqTools::App::reads_long_gaps_size_distribution Measure size distribution of long alignment gaps produced by a gap aware aligner.     0.1.8
CLIPSeqTools::App::size_distribution Measure size distribution for reads.     0.1.8
CLIPSeqTools::CompareApp A collection of tools to compare two CLIP-Seq libraries.     0.1.8
CLIPSeqTools::CompareApp::all Run all clipseqtools-compare analyses.     0.1.8
CLIPSeqTools::CompareApp::compare_counts Compare tables with counts.     0.1.8
CLIPSeqTools::CompareApp::join_tables Perform inner join on tab delimited table files. Can be used to prepare DESeq input file from counts tables.     0.1.8
CLIPSeqTools::CompareApp::libraries_overlap_stats Count reads of library A that overlap reads in reference library B.     0.1.8
CLIPSeqTools::CompareApp::libraries_relative_read_density Measure read density around the reads of a reference library     0.1.8
CLIPSeqTools::PlotApp Tools to create plots based on the output of CLIPSeqTools applications.     0.1.8
CLIPSeqTools::PlotApp::cluster_size_and_score_distribution Create plots for script cluster_size_and_score_distribution.     0.1.8
CLIPSeqTools::PlotApp::conservation_distribution Create plots for script conservation_distribution.     0.1.8
CLIPSeqTools::PlotApp::distribution_on_genic_elements Create plots for script distribution_on_genic_elements.     0.1.8
CLIPSeqTools::PlotApp::distribution_on_introns_exons Create plots for script distribution_on_introns_exons.     0.1.8
CLIPSeqTools::PlotApp::genomic_distribution Create plots for script genomic_distribution.     0.1.8
CLIPSeqTools::PlotApp::libraries_relative_read_density Create plots for script libraries_relative_read_density.     0.1.8
CLIPSeqTools::PlotApp::nucleotide_composition Create plots for script nucleotide_composition.     0.1.8
CLIPSeqTools::PlotApp::reads_long_gaps_size_distribution Create plots for script reads_long_gaps_size_distribution.     0.1.8
CLIPSeqTools::PlotApp::scatterplot Create scatterplot for two tables.     0.1.8
CLIPSeqTools::PlotApp::size_distribution Create plots for script size_distribution.     0.1.8
CLIPSeqTools::PreprocessApp Tools to process a fastq file with CLIP-Seq data into a database compatible with clipseqtools.     0.1.8
CLIPSeqTools::PreprocessApp::all Run all clipseqtools-preprocess analyses.     0.1.8
CLIPSeqTools::PreprocessApp::annotate_with_conservation Annotate alignments in a database table with conservation scores.     0.1.8
CLIPSeqTools::PreprocessApp::annotate_with_deletions Annotate alignments in a database table with deletions.     0.1.8
CLIPSeqTools::PreprocessApp::annotate_with_file Annotate alignments in a database table with regions from a BED/SAM file.     0.1.8
CLIPSeqTools::PreprocessApp::annotate_with_genic_elements Annotate alignments in a database table with genic information.     0.1.8
CLIPSeqTools::PreprocessApp::cleanup_alignment Keep a single record for multimappers, sort and collapse similar STAR alignments.     0.1.8
CLIPSeqTools::PreprocessApp::collapse_fastq Keep a single record for identical sequences     0.1.8
CLIPSeqTools::PreprocessApp::cut_adaptor Cut the adaptor sequence from the 3'end of reads.     0.1.8
CLIPSeqTools::PreprocessApp::sam_to_sqlite Load a SAM file in an SQLite database.     0.1.8
CLIPSeqTools::PreprocessApp::star_alignment Do reads alignment with STAR.     0.1.8
CLIPSeqTools::PreprocessApp::trim_fastq Trim N nucleotides from the start and/or end of FASTQ sequences.     0.1.8
CLIPSeqTools::Role::Option::Genes Role to enable reading a GTF file with genes/transcripts from the command line     0.1.8
CLIPSeqTools::Role::Option::Library Role to enable reading a library with reads from the command line     0.1.8
CLIPSeqTools::Role::Option::OutputPrefix Role to enable output prefix as command line option.     0.1.8
CLIPSeqTools::Role::Option::Plot Role to enable plot as command line option     0.1.8
CLIPSeqTools::Role::Option::ReferenceLibrary Role to enable reading reference libraries with reads from the command line     0.1.8
CLIPSeqTools::Role::Option::Transcripts Role to enable reading a GTF file with transcripts from the command line     0.1.8


CLIPSeqTools::Tutorial::Details A detailed description of *CLIPSeqTools*  
CLIPSeqTools::Tutorial::Introduction An introduction to *CLIPSeqTools*  

Other Files