CLIPSeqTools 1.0.0
- Released by
- MNSMAR
- Version
- Release Date
- 2022-01-31
- Kwalitee
- 146.88
- Core Kwalitee
- 93.75
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CLIPSeqTools 1.0.0 Latest
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Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| CLIPSeqTools | A collection of tools for the analysis of CLIP-Seq data. | 1.0 | metacpan |
| CLIPSeqTools::App | Main CLIPSeqTools application with tools for analysis of CLIP-Seq libraries. | 1.0 | metacpan |
| CLIPSeqTools::App::all | Run all clipseqtools analyses | 1.0 | metacpan |
| CLIPSeqTools::App::cluster_size_and_score_distribution | Assemble reads in clusters and measure their size and number of contained reads distribution | 1.0 | metacpan |
| CLIPSeqTools::App::conservation_distribution | Measure reads at each conservation level | 1.0 | metacpan |
| CLIPSeqTools::App::count_reads_on_genic_elements | Count reads on transcripts, genes, exons, introns | 1.0 | metacpan |
| CLIPSeqTools::App::distribution_on_genic_elements | Measure read distribution on 5'UTR, CDS and 3'UTR. | 1.0 | metacpan |
| CLIPSeqTools::App::distribution_on_introns_exons | Measure read distribution on exons and introns. | 1.0 | metacpan |
| CLIPSeqTools::App::export_bed | Export reads to a BED file. | 1.0 | metacpan |
| CLIPSeqTools::App::genome_coverage | Measure percent of genome covered by reads. | 1.0 | metacpan |
| CLIPSeqTools::App::genomic_distribution | Count reads on genes, repeats, exons, introns, 5'UTRs, ... | 1.0 | metacpan |
| CLIPSeqTools::App::nmer_enrichment_over_shuffled | Measure Nmer enrichment over shuffled reads. | 1.0 | metacpan |
| CLIPSeqTools::App::nucleotide_composition | Measure nucleotide composition along reads. | 1.0 | metacpan |
| CLIPSeqTools::App::reads_long_gaps_size_distribution | Measure size distribution of long alignment gaps produced by a gap aware aligner. | 1.0 | metacpan |
| CLIPSeqTools::App::size_distribution | Measure size distribution for reads. | 1.0 | metacpan |
| CLIPSeqTools::CompareApp | A collection of tools to compare two CLIP-Seq libraries. | 1.0 | metacpan |
| CLIPSeqTools::CompareApp::all | Run all clipseqtools-compare analyses. | 1.0 | metacpan |
| CLIPSeqTools::CompareApp::compare_counts | Compare tables with counts. | 1.0 | metacpan |
| CLIPSeqTools::CompareApp::join_tables | Perform inner join on tab delimited table files. Can be used to prepare DESeq input file from counts tables. | 1.0 | metacpan |
| CLIPSeqTools::CompareApp::libraries_overlap_stats | Count reads of library A that overlap reads in reference library B. | 1.0 | metacpan |
| CLIPSeqTools::CompareApp::libraries_relative_read_density | Measure read density around the reads of a reference library | 1.0 | metacpan |
| CLIPSeqTools::PlotApp | Tools to create plots based on the output of CLIPSeqTools applications. | 1.0 | metacpan |
| CLIPSeqTools::PlotApp::cluster_size_and_score_distribution | Create plots for script cluster_size_and_score_distribution. | 1.0 | metacpan |
| CLIPSeqTools::PlotApp::conservation_distribution | Create plots for script conservation_distribution. | 1.0 | metacpan |
| CLIPSeqTools::PlotApp::distribution_on_genic_elements | Create plots for script distribution_on_genic_elements. | 1.0 | metacpan |
| CLIPSeqTools::PlotApp::distribution_on_introns_exons | Create plots for script distribution_on_introns_exons. | 1.0 | metacpan |
| CLIPSeqTools::PlotApp::genomic_distribution | Create plots for script genomic_distribution. | 1.0 | metacpan |
| CLIPSeqTools::PlotApp::libraries_relative_read_density | Create plots for script libraries_relative_read_density. | 1.0 | metacpan |
| CLIPSeqTools::PlotApp::nucleotide_composition | Create plots for script nucleotide_composition. | 1.0 | metacpan |
| CLIPSeqTools::PlotApp::reads_long_gaps_size_distribution | Create plots for script reads_long_gaps_size_distribution. | 1.0 | metacpan |
| CLIPSeqTools::PlotApp::scatterplot | Create scatterplot for two tables. | 1.0 | metacpan |
| CLIPSeqTools::PlotApp::size_distribution | Create plots for script size_distribution. | 1.0 | metacpan |
| CLIPSeqTools::PreprocessApp | Tools to process a fastq file with CLIP-Seq data into a database compatible with clipseqtools. | 1.0 | metacpan |
| CLIPSeqTools::PreprocessApp::all | Run all clipseqtools-preprocess analyses. | 1.0 | metacpan |
| CLIPSeqTools::PreprocessApp::annotate_with_conservation | Annotate alignments in a database table with conservation scores. | 1.0 | metacpan |
| CLIPSeqTools::PreprocessApp::annotate_with_deletions | Annotate alignments in a database table with deletions. | 1.0 | metacpan |
| CLIPSeqTools::PreprocessApp::annotate_with_file | Annotate alignments in a database table with regions from a BED/SAM file. | 1.0 | metacpan |
| CLIPSeqTools::PreprocessApp::annotate_with_genic_elements | Annotate alignments in a database table with genic information. | 1.0 | metacpan |
| CLIPSeqTools::PreprocessApp::cleanup_alignment | Keep a single record for multimappers, sort and collapse similar STAR alignments. | 1.0 | metacpan |
| CLIPSeqTools::PreprocessApp::collapse_fastq | Keep a single record for identical sequences | 1.0 | metacpan |
| CLIPSeqTools::PreprocessApp::cut_adaptor | Cut the adaptor sequence from the 3'end of reads. | 1.0 | metacpan |
| CLIPSeqTools::PreprocessApp::sam_to_sqlite | Load a SAM file in an SQLite database. | 1.0 | metacpan |
| CLIPSeqTools::PreprocessApp::star_alignment | Do reads alignment with STAR. | 1.0 | metacpan |
| CLIPSeqTools::PreprocessApp::trim_fastq | Trim N nucleotides from the start and/or end of FASTQ sequences. | 1.0 | metacpan |
| CLIPSeqTools::Role::Option::Genes | Role to enable reading a GTF file with genes/transcripts from the command line | 1.0 | metacpan |
| CLIPSeqTools::Role::Option::Library | Role to enable reading a library with reads from the command line | 1.0 | metacpan |
| CLIPSeqTools::Role::Option::OutputPrefix | Role to enable output prefix as command line option. | 1.0 | metacpan |
| CLIPSeqTools::Role::Option::Plot | Role to enable plot as command line option | 1.0 | metacpan |
| CLIPSeqTools::Role::Option::ReferenceLibrary | Role to enable reading reference libraries with reads from the command line | 1.0 | metacpan |
| CLIPSeqTools::Role::Option::Transcripts | Role to enable reading a GTF file with transcripts from the command line | 1.0 | metacpan |