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Bio-Graphics-2.40
River stage one • 2 direct dependents • 2 total dependents
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Changes for version 2.40

  • Add CGI as a requirement as it is not part of core perl distributions, post-5.21
  • Add Bio::Coordinate::Pair as a requirement (now released separately from BioPerl core)

Documentation

search_overview
Render a SearchIO parser report into a simple overview graphic
feature_draw.pl
Render a Bio::Graphics Feature File
frend.pl
Render a Bio::Graphics Feature File on the web
search_overview
Render a SearchIO parser report into a simple overview graphic

Modules

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

Provides

Bio::Graphics::FileSplitter
in lib/Bio/Graphics/FeatureDir.pm
Bio::Graphics::GDWrapper
in lib/Bio/Graphics/GDWrapper.pm
Bio::Graphics::Glyph::cross
in lib/Bio/Graphics/Glyph/cross.pm
Bio::Graphics::Glyph::fb_shmiggle
in lib/Bio/Graphics/Glyph/fb_shmiggle.pm
Bio::Graphics::Glyph::point_glyph
in lib/Bio/Graphics/Glyph/point_glyph.pm
Bio::Graphics::Glyph::read_pair
in lib/Bio/Graphics/Glyph/read_pair.pm
Bio::Graphics::Glyph::smoothing
in lib/Bio/Graphics/Glyph/smoothing.pm
Bio::Graphics::Glyph::topoview
in lib/Bio/Graphics/Glyph/topoview.pm
Bio::Graphics::Glyph::wiggle_data
in lib/Bio/Graphics/Glyph/wiggle_data.pm
Bio::Graphics::Glyph::wiggle_whiskers
in lib/Bio/Graphics/Glyph/wiggle_whiskers.pm
Bio::Graphics::Layout
in lib/Bio/Graphics/Layout.pm
Bio::Graphics::Layout::Contour
in lib/Bio/Graphics/Layout.pm
Bio::Graphics::Math
in lib/Bio/Graphics/Layout.pm
Bio::Graphics::Wiggle::Loader
in lib/Bio/Graphics/Wiggle/Loader.pm

Examples

Other files