Uses of Class
org.snpeff.SnpEff
Packages that use SnpEff
-
Uses of SnpEff in org.snpeff
Fields in org.snpeff declared as SnpEffMethods in org.snpeff that return SnpEffMethods in org.snpeff with parameters of type SnpEffModifier and TypeMethodDescriptionprotected booleanSnpEff.run(SnpEff snpEff, String[] args, StringBuilder err) Run a SnpEff (usually a sub-class) -
Uses of SnpEff in org.snpeff.snpEffect.commandLine
Subclasses of SnpEff in org.snpeff.snpEffect.commandLineModifier and TypeClassDescriptionclassACAT: Create ACAT score for T2D project Note: This is just used to compile 'ACAT' score in T2D-GENES project, not useful at all for general audience.classCommand line program: Build databaseclassParse NetxProt XML file and build a database http://www.nextprot.org/classCommand line: Calculate coding sequences from a file and compare them to the ones calculated from our data structuresclassCommand line: Find closes marker to each variantclassCount reads from a BAM file given a list of intervalsclassShow all databases configures in snpEff.config Create an HTML 'download' table based on the config file Also creates a list of genome for Galaxy menuclassCommand line program: Download and install a (pre built) databaseclassCommand line program: Build databaseclassCommand line program: Predict variant effectsclassSimple test programclassCommand line: Gene-Sets Analysis Perform gene set analysysclassCalculate the maximum interval length by type, for all markers in a genomeclassPDB distance analysisclassCommand line: Read protein sequences from a file and compare them to the ones calculated from our data structures Note: This is done in order to see potential incompatibility errors between genome sequence and annotation.classCommand line program: Show a transcript or a geneclassCommand line program: Show a transcript or a geneclassCreate an SVG representation of a Marker -
Uses of SnpEff in org.snpeff.spliceSites
Subclasses of SnpEff in org.snpeff.spliceSitesModifier and TypeClassDescriptionclassAnalyze sequences from splice sites