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



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