Package edu.cornell.med.icb.tissueinfo.similarity

Tools to calculate tissue expression profile similarity.

See:
Description

Interface Summary

EstMatch2Counts

Class Summary

AllenGeneAtlas2Counts	Converts expression data from the Allen Gene Atlas to TEPSS counts.
AnnotateClustersMode	Calculates tissue weights for a set of clusters generated by ClusterMode.
BackwardMode	Backward tiSimilarity screen.
ClusterMode
CrossValidationMode	Splits a dataset into a number of categories and performs cross validation with forward mode.
EstMatch2CuratedCancerTissueCounts
EstMatch2CuratedCancerTissueOnlyCounts
EstMatch2CuratedNormalTissueOnlyCounts
EstMatch2CuratedTissueCounts
EstMatch2RawTissueCounts
ForwardMode
GeneTranscriptRelationships
GroupScoringMode
LeaveOneOutMode	Performs leave-one-out with forward mode.
ListSearchMode	Scan a list of accession codes.
PairScoreOnlyMode
PairSearchMode
ScoredTranscriptBoundedSizeQueue	This class is an adaptation of MG4J's DocumentScoreBoundedSizeQueue.
SimpleSearchMode	Search one accession code against the rest of the transcriptome.
TallyScoreSearchMode	Perform a genome x genome search and tally the number of scores that fit into configurable score bins.
TiDumpTissueCounts	Process one or several tiac file(s) to dump tissue EST counts for each sequence represented in the tiac file(s).
TiSimilarity	Given sequence accession codes, produces a ranked list of sequences with similar tissue expression profile.
TiSimilarityLocalCopy	Given sequence accession codes, produces a ranked list of sequences with similar tissue expression profile.
TiSimilaritySearchEngine
TiSimMode
TiSimOptions	Regroups options for tiSimilarity.
TissueESTCountsHelper	Helper class to access Tissue EST counts.
TissueESTCountsReader	Reads compressed counts data for a set of query sequences.
TissueESTCountsWriter	Writes a compressed file with information about EST counts for a set of transcripts.
TiWeights
TranscriptListMode	Created by IntelliJ IDEA.
TranscriptScore

Package edu.cornell.med.icb.tissueinfo.similarity Description

Tools to calculate tissue expression profile similarity. See the TissueInfo page on the ICB wiki for rational and uses.

Package Specification

Related Documentation