4DNucleomeAnalysisToolbox.prj

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    <param.appname>4D Nucleome Analysis Toolbox</param.appname>
    <param.authnamewatermark>Laura Seaman</param.authnamewatermark>
    <param.email>laseaman@umich.edu</param.email>
    <param.company>University of Michigan</param.company>
    <param.summary>NAT includes functions to load Hi-C data from text files, normalization, TAD detection, and plotting.</param.summary>
    <param.description>examples available at: https:/laseaman/4D_Nucleome_Analysis_Toolbox</param.description>
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    <param.exclude.filters>% List files contained in your toolbox folder that you would like to exclude
% from packaging.  Excludes should be listed relative to the toolbox folder.
% Some examples of how to specify excludes are provided below:
%
% A single file in the toolbox folder:
% .svn
%
% A single file in a subfolder of the toolbox folder:
% example/.svn
%
% All files in a subfolder of the toolbox folder:
% example/*
%
% All files of a certain name in all subfolders of the toolbox folder:
% **/.svn
%
% All files matching a pattern in all subfolders of the toolbox folder:
% **/*.bak
%

.DS_Store</param.exclude.filters>
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      <file>${PROJECT_ROOT}/NAT_functions</file>
    </fileset.rootdir>
    <fileset.rootfiles>
      <file>${PROJECT_ROOT}/NAT_functions/AddCent.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/BlockToepNorm.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/DIndex.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/Draw_TADs.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/FindGenLocation.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/FindGenbin.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/HiC_load_cool.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/HiC_load_mat.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/HiC_plot.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/HiC_remove_cent.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/HicRna_plot.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/HicTensorFig.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/ICE.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/Load_TSV.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/Mat2Val.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/Mean_density.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/PltFV.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/PltPhasePlane.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/RNA2Bin.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/Scaled_density.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/TADMark2Pos_HMM.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/TAD_DP1.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/TAD_HMM.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/TAD_Laplace.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/ToepNorm.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/TranslocHiC.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/arrow.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/bar3_custom.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/cbar.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/em_converged.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/fwdback.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/gaussian_prob.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/isposdef.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/logdet.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/mhmm_em.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/mixgauss_Mstep.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/mixgauss_prob.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/mk_stochastic.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/normalise.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/process_options.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/saveHiC.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/saveTADs.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/sqdist.m</file>
      <file>${PROJECT_ROOT}/NAT_functions/sumDiag.m</file>
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