Code covered by the BSD License
Highlights from
MotifCatcher
- MC_TreeWithClusters(phytree,T... This function allows for interactive user-control of phytree, and draw
- MC_inputSearchStyle function: when gathering inputs, this block allows the user to specify a
- MotifCatcher An introductory GUI welcomes the user to MotifCatcher, and allows he or
- ... Description:
- MC_CompareOccurrenceAndLocali... This function determines the significant co-occurrence / co-localizations
- MC_GetFPDir Description: input-gathering function for FP directory.
- MC_GetFamilies(STAMPTreeClust... This function retrieves families of End States from STAMP's Clustering
- MC_GetInput_MakeMotifTree(Sou... Description: gather input parameters required for converting a library of
- MC_GetInput_MakeRelatedSubsets Description: function that gathers all input parameters required to make
- MC_GetMotif(file) This function extracts a motif from a given meme.txt file.
- MC_GetMotifTreeDir Description: gather inputs for retrieving motif tree information, for
- MC_GetR(RDirectory) Description: This function determines the appropriate related subsets
- MC_GetRegularExpression(file) This function returns a regular expression string from a meme output file.
- MC_GetSharedSites(AllMotifsAn... This function creates a list of sequence entries from a MM-like structure
- MC_GetSubsetList(mastdirector... Extract list of sequence entries from a mast .txt output file. The format of the
- MC_GetTransfacPWMs(DirectoryL... Description:
- MC_MakeClusters(DataSetProfil... (1) Compute clusters and retrieve Motif Tree
- MC_MakeFPs(AllMotifsAndLocati... Description: This function creates FPs from the GUI tree viewer.
- MC_MakeMembershipMatrix(Input... This function produces a membership matrix for cases where top motifs are
- MC_MakeMembershipMatrixwHeade... This function produces a membership matrix for cases where top motifs are
- MC_MakeMotifMap(Directories,S... After clusters, families, etc have been determined on a given dataset,
- MC_MakeMotifTree(DataSetProfi... Description: this function creates a motif tree from the motifs associated
- MC_MotifCatcherPipeline(TaskN... This function performs the entire 'MotifCatcher' analysis on an input
- MC_ProceedToNextStep description: GUI dialog box, ask user if they would like to continue to
- MC_ViewFPs(Directory) This function views all generated FPs for a particular directory.
- MC_ViewFamilyMembers(AllMotif... This function views all Ri within a single family.
- MC_WholePipelineViewResults description: following a whole pipeline run, you may review the results in
- [SeqFile Directories MEME_par... Description: retrieve input parameters for whole pathway
- [SubsetList MEME_parameters]=... This function generates Ri according to one of the three R-determination
- Make_Synthetic_Data.m
- View all files
MotifCatcher
06 Jul 2011 (Updated 17 Nov 2011) a MATLAB GUI platform for determination and evaluation of biologically significant motifs |
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