Bio-Tradis 1.4.1
Kwalitee Issues
- has_changelog
-
Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.
- use_strict
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Add 'use strict' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules are strictly written.
Error: Bio::Tradis::Analysis::Exceptions, Bio::Tradis::Exception
- meta_yml_declares_perl_version
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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.
- use_warnings
-
Add 'use warnings' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.
Error: Bio::Tradis::Analysis::Exceptions, Bio::Tradis::Exception
Modules
Name | Abstract | Version | View |
---|---|---|---|
Bio::Tradis | Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308 | v1.4.1 | metacpan |
Bio::Tradis::AddTagsToSeq | Takes a BAM file and creates a new BAM with tr and tq tags added to the sequence and quality strings. | v1.4.1 | metacpan |
Bio::Tradis::Analysis::Exceptions | Custom exceptions | v1.4.1 | metacpan |
Bio::Tradis::Analysis::InsertSite | Take in a bam file and plot the start position of each read | v1.4.1 | metacpan |
Bio::Tradis::CombinePlots | Combine multiple plotfiles and generate updated statistics for the combined files | v1.4.1 | metacpan |
Bio::Tradis::CommandLine::AddTags | Add given tags to the start of the sequence | v1.4.1 | metacpan |
Bio::Tradis::CommandLine::CheckTags | Check for presence of tr tag in BAM file | v1.4.1 | metacpan |
Bio::Tradis::CommandLine::FilterFastqTags | Remove given tags from the start of the sequence | v1.4.1 | metacpan |
Bio::Tradis::CommandLine::PlotCombine | Combine multiple plotfiles and generate updated statistics for the combined files | v1.4.1 | metacpan |
Bio::Tradis::CommandLine::PlotTradis | Generate plots as part of a tradis analysis | v1.4.1 | metacpan |
Bio::Tradis::CommandLine::RemoveFastqTags | Remove given tags from the start of the sequence | v1.4.1 | metacpan |
Bio::Tradis::CommandLine::RunMapping | Perform mapping | v1.4.1 | metacpan |
Bio::Tradis::CommandLine::TradisAnalysis | Perform full tradis analysis | v1.4.1 | metacpan |
Bio::Tradis::CommandLine::TradisBam | Adds tags to sequences if tags are present | v1.4.1 | metacpan |
Bio::Tradis::DetectTags | Detect tr tags in BAM file | v1.4.1 | metacpan |
Bio::Tradis::Exception | Exceptions for input data | v1.4.1 | metacpan |
Bio::Tradis::FilterTags | Filter tags in a fastq file | v1.4.1 | metacpan |
Bio::Tradis::Map | Perform mapping | v1.4.1 | metacpan |
Bio::Tradis::Parser::Bam | Very basic BAM parser. Limited functionality. | v1.4.1 | metacpan |
Bio::Tradis::Parser::Cigar | Take in a cigar string and output start and end relative to the reference sequence | v1.4.1 | metacpan |
Bio::Tradis::Parser::Fastq | Basic FastQ parser. | v1.4.1 | metacpan |
Bio::Tradis::RemoveTags | Remove tags from seqs a fastq file | v1.4.1 | metacpan |
Bio::Tradis::RunTradis | Perform all steps required for a tradis analysis | v1.4.1 | metacpan |
Bio::Tradis::Samtools | Change samtools syntax depending on version found | v1.4.1 | metacpan |
Bio::Tradis::TradisPlot | Generate plots as part of a tradis analysis | v1.4.1 | metacpan |