Bio-ViennaNGS v0.19
- Released by
- MTW
- Version
- Release Date
- 2018-07-03
- Kwalitee
- 146.88
- Core Kwalitee
- 93.75
- LINKS
Bio-ViennaNGS v0.19
Kwalitee Issues
- use_strict
-
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::ViennaNGS
- no_pod_errors
-
Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.
Error: Bio-ViennaNGS-v0.19/scripts/Tutorial_pipeline03.pl -- Around line 176: You forgot a '=back' before '=head1' Bio-ViennaNGS-v0.19/scripts/trim_fastq.pl -- Around line 134: Unknown directive: =over1 Around line 136: '=item' outside of any '=over'
- 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::ViennaNGS
- no_invalid_versions
-
Fix the version numbers so that version::is_lax($version) returns true.
Error:
- lib/Bio/ViennaNGS/AnnoC.pm: HASH(0x55607ced0190)
- lib/Bio/ViennaNGS/Bam.pm: HASH(0x55607ce6f938)
- lib/Bio/ViennaNGS/Bed.pm: HASH(0x55607cedf808)
- lib/Bio/ViennaNGS/BedGraphEntry.pm: HASH(0x55607c495620)
- lib/Bio/ViennaNGS/Expression.pm: HASH(0x55607ce87210)
- lib/Bio/ViennaNGS/ExtFeature.pm: HASH(0x55607b4d3828)
- lib/Bio/ViennaNGS/Fasta.pm: HASH(0x55607ce6a248)
- lib/Bio/ViennaNGS/Feature.pm: HASH(0x55607ce61518)
- lib/Bio/ViennaNGS/FeatureChain.pm: HASH(0x55607cec10e0)
- lib/Bio/ViennaNGS/FeatureIO.pm: HASH(0x55607cec1368)
- lib/Bio/ViennaNGS/FeatureInterval.pm: HASH(0x55607ce70310)
- lib/Bio/ViennaNGS/FeatureIntervalN.pm: HASH(0x55607ceed640)
- lib/Bio/ViennaNGS/FeatureLine.pm: HASH(0x55607ce93db0)
- lib/Bio/ViennaNGS/MinimalFeature.pm: HASH(0x55607ce611e8)
- lib/Bio/ViennaNGS/Peak.pm: HASH(0x55607ce61218)
- lib/Bio/ViennaNGS/SpliceJunc.pm: HASH(0x55607ce61b18)
- lib/Bio/ViennaNGS/Subtypes.pm: HASH(0x55607c4465e0)
- lib/Bio/ViennaNGS/Tutorial.pm: HASH(0x55607ceb1b20)
- lib/Bio/ViennaNGS/UCSC.pm: HASH(0x55607cebaf88)
- lib/Bio/ViennaNGS/Util.pm: HASH(0x55607ce69fd8)
- 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.
- meta_yml_has_repository_resource
-
Add a 'repository' resource to the META.yml via 'meta_add' accessor (for Module::Build) or META_ADD parameter (for ExtUtils::MakeMaker).
- has_separate_license_file
-
This is not a critical issue. Currently mainly informative for the CPANTS authors. It might be removed later.
Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| Bio::ViennaNGS | A Perl distribution for Next-Generation Sequencing (NGS) data analysis | 0.019000 | metacpan |
| Bio::ViennaNGS::AnnoC | Object-oriented interface for storing and converting biological sequence annotation formats | metacpan | |
| Bio::ViennaNGS::Bam | High-level access to BAM files | metacpan | |
| Bio::ViennaNGS::Bed | Object-oriented interface for manipulation of genomic interval data in BED format | metacpan | |
| Bio::ViennaNGS::BedGraphEntry | metacpan | ||
| Bio::ViennaNGS::Expression | An object oriented interface for computing read-count based gene expression as TPM or RPKM | metacpan | |
| Bio::ViennaNGS::ExtFeature | A Moose wrapper for extended BED6-type genomic intervals. | metacpan | |
| Bio::ViennaNGS::Fasta | Moose wrapper for Bio::DB::Fasta | metacpan | |
| Bio::ViennaNGS::Feature | A Moose wrapper for BED6-type genomic intervals. | metacpan | |
| Bio::ViennaNGS::FeatureChain | Generic Moose wrapper class for combined/linked genomic intervals, eg BED12 elements | metacpan | |
| Bio::ViennaNGS::FeatureIO | Versatile I/O interface for Bio::ViennaNGS feature annotation classes | metacpan | |
| Bio::ViennaNGS::FeatureInterval | A Moose class for unstranded, elementary genomic intervals. | metacpan | |
| Bio::ViennaNGS::FeatureIntervalN | A Moose wrapper for named genomic intervals. | metacpan | |
| Bio::ViennaNGS::FeatureLine | metacpan | ||
| Bio::ViennaNGS::MinimalFeature | A Moose wrapper for stranded genomic intervals. | metacpan | |
| Bio::ViennaNGS::Peak | An object oriented interface for characterizing peaks in RNA-seq data | metacpan | |
| Bio::ViennaNGS::SpliceJunc | Perl extension for alternative splicing analysis | metacpan | |
| Bio::ViennaNGS::Subtypes | metacpan | ||
| Bio::ViennaNGS::Tutorial | A collection of basic tutorials demonstrating of the core components and features of the L<Bio::ViennaNGS> suite | metacpan | |
| Bio::ViennaNGS::UCSC | Perl extension for easy UCSC Genome Browser integration. | metacpan | |
| Bio::ViennaNGS::Util | Utility routines for Next-Generation Sequencing data analysis | metacpan |