Kwalitee Issues

has_changelog

Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.

package_version_matches_dist_version

Fix the version(s).

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::PanGenome::Exceptions

has_meta_json

Add a META.json to the distribution. Your buildtool should be able to autogenerate it.

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.

use_warnings

Add 'use warnings' (or its equivalents) to all modules (this will require perl > 5.6), 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::PanGenome::Exceptions

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
Bio::PanGenome Create a pan genome metacpan
Bio::PanGenome::AnalyseGroups Take in a groups file and the original FASTA files and create plots and stats metacpan
Bio::PanGenome::AnnotateGroups Take in a group file and assosiated GFF files for the isolates and update the group name to the gene name metacpan
Bio::PanGenome::ChunkFastaFile Take in a FASTA file and chunk it up into smaller pieces. metacpan
Bio::PanGenome::ClustersRole A role to read a clusters file from CD hit metacpan
Bio::PanGenome::CombinedProteome Take in multiple FASTA sequences containing proteomes and concat them together and output a FASTA file, filtering out more than 5% X's metacpan
Bio::PanGenome::CommandLine::CreatePanGenome Take in FASTA files of proteins and cluster them metacpan
Bio::PanGenome::CommandLine::ExtractProteomeFromGff Take in GFF files and output the proteome metacpan
Bio::PanGenome::CommandLine::PanGenomePostAnalysis Perform the post analysis on the pan genome metacpan
Bio::PanGenome::CommandLine::PanGenomeReorderSpreadsheet Take in a tree and a spreadsheet and output a reordered spreadsheet metacpan
Bio::PanGenome::CommandLine::ParallelAllAgainstAllBlastp Take in a FASTA file of proteins and blast against itself metacpan
Bio::PanGenome::CommandLine::PlotPanGenomeGroups Take in the groups file and output some summary plots metacpan
Bio::PanGenome::CommandLine::QueryPanGenome Take in a groups file and the protein fasta files and output selected data metacpan
Bio::PanGenome::CommandLine::TransferAnnotationToGroups Take in a groups file and a set of GFF files and transfer the consensus annotation metacpan
Bio::PanGenome::Exceptions Exceptions for input data metacpan
Bio::PanGenome::External::Blastp Wrapper around NCBIs blastp command metacpan
Bio::PanGenome::External::Cdhit Wrapper to run cd-hit metacpan
Bio::PanGenome::External::Makeblastdb Wrapper around NCBIs makeblastdb command metacpan
Bio::PanGenome::External::Mcl Wrapper around MCL which takes in blast results and outputs clustered results metacpan
Bio::PanGenome::External::Muscle Wrapper around Muscle for sequence alignment metacpan
Bio::PanGenome::External::PostAnalysis Perform the post analysis metacpan
Bio::PanGenome::External::Segmasker Wrapper around Segmasker for low complexity filtering metacpan
Bio::PanGenome::ExtractProteomeFromGFF Take in a GFF file and create protein sequences in FASTA format metacpan
Bio::PanGenome::ExtractProteomeFromGFFs Take in GFF files and create protein sequences in FASTA format metacpan
Bio::PanGenome::FilterFullClusters Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters metacpan
Bio::PanGenome::FilterUnknownsFromFasta Take in fasta files, remove sequences with too many unknowns and return a list of the new files metacpan
Bio::PanGenome::GeneNamesFromGFF Parse a GFF and efficiently extract ID -> Gene Name metacpan
Bio::PanGenome::GroupLabels Add labels to the groups metacpan
Bio::PanGenome::GroupStatistics Add labels to the groups metacpan
Bio::PanGenome::InflateClusters Take the clusters file from cd-hit and use it to inflate the output of MCL metacpan
Bio::PanGenome::JobRunner::LSF Execute a set of commands using LSF metacpan
Bio::PanGenome::JobRunner::Local Execute a set of commands locally metacpan
Bio::PanGenome::JobRunner::Role A role to add job runner functionality metacpan
Bio::PanGenome::Output::DifferenceBetweenSets Given two sets of isolates and a group file, output whats unique in each and whats in common metacpan
Bio::PanGenome::Output::GroupMultifasta Take in a group and create a multifasta file metacpan
Bio::PanGenome::Output::GroupTabFiles Take in an array of files and output raw tab files for analysis by R to turn into plots metacpan
Bio::PanGenome::Output::GroupsMultifastaNucleotide Take in a GFF files and a groups file and output one multifasta file per group with nucleotide sequences. metacpan
Bio::PanGenome::Output::GroupsMultifastas Take in a list of groups and create multifastas files for each group metacpan
Bio::PanGenome::Output::GroupsMultifastasNucleotide Take in a set of GFF files and a groups file and output one multifasta file per group with nucleotide sequences. metacpan
Bio::PanGenome::Output::NumberOfGroups Create raw output files of group counts for turning into plots metacpan
Bio::PanGenome::Output::OneGenePerGroupFasta Output a fasta file with one gene per group metacpan
Bio::PanGenome::Output::QueryGroups Output the groups of the union of a set of input isolates metacpan
Bio::PanGenome::ParallelAllAgainstAllBlast Run all against all blast in parallel metacpan
Bio::PanGenome::Plot::FreqOfGenes Take in an array of frequencies of groups and output a plot metacpan
Bio::PanGenome::PostAnalysis Post analysis of pan genomes metacpan
Bio::PanGenome::PrepareInputFiles Take in a mixture of FASTA and GFF input files and output FASTA proteomes only metacpan
Bio::PanGenome::ReorderSpreadsheet Take in a tree file and a spreadsheet and output a spreadsheet with reordered columns metacpan
Bio::PanGenome::SampleOrder Take in a tree file and return an ordering of the samples metacpan
Bio::PanGenome::SequenceLengths Take in a fasta file and create a hash with the length of each sequence metacpan

Other Files

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