📦 libbio-graphics-perl

104 pages

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Bio::Graphics(3pm)Generate GD images of Bio::Seq objects✨
Bio::Graphics::ConfiguratorI(3pm)A sectioned map of configuration options (a map of maps), with a default section. Intended to augment existing tag->value semantics (ie. of Bio::AnnotationCollectionI) for object-representation…✨
Bio::Graphics::DrawTransmembrane(3pm)draw a cartoon of an Alpha-helical transmembrane protein.✨
Bio::Graphics::Feature(3pm)A simple feature object for use with Bio::Graphics::Panel✨
Bio::Graphics::FeatureBase(3pm)Compatibility module✨
Bio::Graphics::FeatureDir(3pm)A directory of feature files and conf files✨
Bio::Graphics::FeatureFile(3pm)A set of Bio::Graphics features, stored in a file✨
Bio::Graphics::FeatureFile::Iterator(3pm)Iterator across a Bio::Graphics::FeatureFile✨
Bio::Graphics::Glyph(3pm)Base class for Bio::Graphics::Glyph objects✨
Bio::Graphics::Glyph::alignment(3pm)The "alignment" glyph✨
Bio::Graphics::Glyph::allele_tower(3pm)The "allele_tower" glyph✨
Bio::Graphics::Glyph::anchored_arrow(3pm)The "anchored_arrow" glyph✨
Bio::Graphics::Glyph::arrow(3pm)the "arrow" glyph✨
Bio::Graphics::Glyph::box(3pm)The "box" glyph✨
Bio::Graphics::Glyph::broken_line(3pm)The "broken line" glyph✨
Bio::Graphics::Glyph::cds(3pm)The "cds" glyph✨
Bio::Graphics::Glyph::christmas_arrow(3pm)The "christmas arrow" glyph✨
Bio::Graphics::Glyph::crossbox(3pm)The "crossbox" glyph✨
Bio::Graphics::Glyph::dashed_line(3pm)The "dashed line" glyph✨
Bio::Graphics::Glyph::decorated_gene(3pm)A GFF3-compatible gene glyph with protein decorations✨
Bio::Graphics::Glyph::decorated_transcript(3pm)draws processed transcript with protein decorations✨
Bio::Graphics::Glyph::diamond(3pm)The "diamond" glyph✨
Bio::Graphics::Glyph::dna(3pm)The "dna" glyph✨
Bio::Graphics::Glyph::dot(3pm)The "dot" glyph✨
Bio::Graphics::Glyph::dumbbell(3pm)A glyph that draws a "dumbbell" with the same shapes on both ends.✨
Bio::Graphics::Glyph::ellipse(3pm)The "ellipse" glyph✨
Bio::Graphics::Glyph::ex(3pm)the "ex", or "crossed box" glyph✨
Bio::Graphics::Glyph::extending_arrow(3pm)The "extending arrow" glyph✨
Bio::Graphics::Glyph::Factory(3pm)Factory for Bio::Graphics::Glyph objects✨
Bio::Graphics::Glyph::fb_shmiggle(3pm)✨
Bio::Graphics::Glyph::fixedwidth(3pm)A base class fixed width glyphs✨
Bio::Graphics::Glyph::flag(3pm)the "flag" glyph✨
Bio::Graphics::Glyph::gene(3pm)A GFF3-compatible gene glyph✨
Bio::Graphics::Glyph::generic(3pm)The "generic" glyph✨
Bio::Graphics::Glyph::graded_segments(3pm)The "graded_segments" glyph✨
Bio::Graphics::Glyph::group(3pm)The "group" glyph✨
Bio::Graphics::Glyph::hat(3pm)The "hat" glyph✨
Bio::Graphics::Glyph::heat_map(3pm)The "heat_map" glyph✨
Bio::Graphics::Glyph::heat_map_ideogram(3pm)The "heat_map_ideogram" glyph✨
Bio::Graphics::Glyph::heterogeneous_segments(3pm)The "heterogeneous_segments" glyph✨
Bio::Graphics::Glyph::hidden(3pm)The "hidden" glyph✨
Bio::Graphics::Glyph::hybrid_plot(3pm)An xyplot plot drawing dual graph using data from two or more wiggle files per track✨
Bio::Graphics::Glyph::ideogram(3pm)The "ideogram" glyph✨
Bio::Graphics::Glyph::image(3pm)A glyph that draws photographs & other images✨
Bio::Graphics::Glyph::lightning(3pm)The "lightning" glyph✨
Bio::Graphics::Glyph::line(3pm)The "line" glyph✨
Bio::Graphics::Glyph::merge_parts(3pm)a base class which suppors semantic zooming of scored alignment features✨
Bio::Graphics::Glyph::merged_alignment(3pm)The "merged_alignment" glyph✨
Bio::Graphics::Glyph::minmax(3pm)The minmax glyph✨
Bio::Graphics::Glyph::operon(3pm)The "polycistronic operon" glyph✨
Bio::Graphics::Glyph::oval(3pm)The "oval" glyph✨
Bio::Graphics::Glyph::pairplot(3pm)The "pairwise plot" glyph✨
Bio::Graphics::Glyph::pentagram(3pm)The "pentagram" glyph✨
Bio::Graphics::Glyph::phylo_align(3pm)The "phylogenetic alignment" glyph✨
Bio::Graphics::Glyph::pinsertion(3pm)The "Drosophila P-element Insertion" glyph✨
Bio::Graphics::Glyph::primers(3pm)The "STS primers" glyph✨
Bio::Graphics::Glyph::processed_transcript(3pm)The sequence ontology transcript glyph✨
Bio::Graphics::Glyph::protein(3pm)The "protein" glyph✨
Bio::Graphics::Glyph::ragged_ends(3pm)The "ragged ends" glyph✨
Bio::Graphics::Glyph::rainbow_gene(3pm)A GFF3-compatible gene glyph✨
Bio::Graphics::Glyph::redgreen_box(3pm)The "redgreen_box" glyph✨
Bio::Graphics::Glyph::redgreen_segment(3pm)The "redgreen_segments" glyph✨
Bio::Graphics::Glyph::repeating_shape(3pm)A glyph that draws the same shape repeatedly.✨
Bio::Graphics::Glyph::rndrect(3pm)The "round rect" glyph✨
Bio::Graphics::Glyph::ruler_arrow(3pm)glyph for drawing an arrow as ruler (5' and 3' are marked as label)✨
Bio::Graphics::Glyph::saw_teeth(3pm)The "saw teeth" glyph✨
Bio::Graphics::Glyph::scale(3pm)The "scale" glyph✨
Bio::Graphics::Glyph::segmented_keyglyph(3pm)The "segmented_keyglyph" glyph✨
Bio::Graphics::Glyph::segments(3pm)The "segments" glyph✨
Bio::Graphics::Glyph::so_transcript(3pm)The sequence ontology transcript glyph✨
Bio::Graphics::Glyph::span(3pm)The "span" glyph✨
Bio::Graphics::Glyph::spectrogram(3pm)The "spectrogram" glyph✨
Bio::Graphics::Glyph::splice_site(3pm)The "splice_site" glyph✨
Bio::Graphics::Glyph::stackedplot(3pm)The stackedplot glyph✨
Bio::Graphics::Glyph::ternary_plot(3pm)Draw ternary plot data✨
Bio::Graphics::Glyph::text_in_box(3pm)The "text in box" glyph✨
Bio::Graphics::Glyph::three_letters(3pm)DAS-compatible package to use for drawing a line of groups of three letters✨
Bio::Graphics::Glyph::tic_tac_toe(3pm)The "tic-tac-toe" glyph✨
Bio::Graphics::Glyph::toomany(3pm)The "too many to show" glyph✨
Bio::Graphics::Glyph::trace(3pm)A glyph that visualizes a trace file✨
Bio::Graphics::Glyph::track(3pm)The "track" glyph✨
Bio::Graphics::Glyph::transcript(3pm)The "transcript" glyph✨
Bio::Graphics::Glyph::transcript2(3pm)The "transcript2" glyph✨
Bio::Graphics::Glyph::translation(3pm)The "6-frame translation" glyph✨
Bio::Graphics::Glyph::triangle(3pm)The "triangle" glyph✨
Bio::Graphics::Glyph::two_bolts(3pm)The "two bolts" glyph✨
Bio::Graphics::Glyph::vista_plot(3pm)The "vista_plot" glyph✨
Bio::Graphics::Glyph::wave(3pm)The "wave" glyph✨
Bio::Graphics::Glyph::weighted_arrow(3pm)The "weighted arrow" glyph✨
Bio::Graphics::Glyph::whiskerplot(3pm)The whiskerplot glyph✨
Bio::Graphics::Glyph::wiggle_box(3pm)A generic box glyph compatible with dense "wig"data✨
Bio::Graphics::Glyph::wiggle_density(3pm)A density plot compatible with dense "wig"data✨
Bio::Graphics::Glyph::wiggle_xyplot(3pm)An xyplot plot compatible with dense "wig"data✨
Bio::Graphics::Glyph::xyplot(3pm)The xyplot glyph✨
Bio::Graphics::Panel(3pm)Generate GD images of Bio::Seq objects✨
Bio::Graphics::Pictogram(3pm)generate SVG output of Pictogram display for consensus motifs✨
Bio::Graphics::RendererI(3pm)A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI objects onto Bio::Graphics::Panels using configuration information provided by a Bio::Graphics::ConfiguratorI.✨
Bio::Graphics::Util(3pm)non-object-oriented utilities used in Bio::Graphics modules ($frame,$offset) = frame_and_offset($pos,$strand,$phase) Calculate the reading frame for a given genomic position, strand and phase. The…✨
Bio::Graphics::Wiggle(3pm)Binary storage for dense genomic features✨
Bio::Graphics::Wiggle::Loader(3pm)✨

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contig_draw(1p)Render a SearchIO parser report into a simple overview graphic✨

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feature_draw(1p)Render a Bio::Graphics Feature File✨
frend(1p)Render a Bio::Graphics Feature File on the web✨

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search_overview(1p)Render a SearchIO parser report into a simple overview graphic✨