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<title>X-CYT: User-guided Automated Flow Cytometric Data Analysis</title>
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<h1 class="about">X-CYT: User-guided Automated Flow Cytometric Data Analysis</h1>

	    <p>
	    <img src="images/xcyt.png" width="500" style="display: block; margin-left: auto; margin-right: auto; box-shadow:3px 3px 3px #888888;"/>
	    </p>

	      
	    <p>X-Cyt follows a user-designed scheme and template to
	    partition cytometric data in two or more dimensions for
	    identifying cell populations of interest. In a small
	    subset of samples, the user may try out several different
	    partitioning schemes, and select one "optimal"
	    partitioning to use as the template to guide the batch
	    analysis of all samples. </p>

	    <p>X-Cyt partitions each sample with initialization by the
	    template, then optimizes on the parameters via
	    estimation-maximization. Template-guided mixture modeling
	    reduces analysis runtime, and simultaneously ensures
	    cross-sample population alignment.</p>

	    <p>The X-Cyt R package has recently been updated to be
            compatible with the latest release of EMMIXskew.</p>

            <p>X-Cyt is developed by Xinli Hu and Hyun Kim in
	      the lab of <a href="/personal/soumya/">
		Soumya Raychaudhuri </a> at the <a href="http://brighamandwomens.org">Brigham and Women's 
		Hospital</a> and <a href="http://hms.harvard.edu">Harvard Medical
		School</a>, and the Broad Institute.</p>

<h2>Links</h2>
	    <ul>
              <li><a href="/mpg/xcyt/code/xcyt_1.3.tar.gz">
		  Download: X-Cyt (R scripts for R-3.0 and later)</a><br/>
	      </li> 
	      <li><a
	    href="http://cran.r-project.org/web/packages/EMMIXskew/index.html">
	          Download: EMMIX-skew R package for your platform (for R-3.0
	    and later)</a><br/>
	      </li>

              <li><a href="/mpg/xcyt/data/CD4TEMData.tar.gz"> 
	         Download: Sample CD4+ Effector Memory T cell
	    dataset (20 samples)</a><br/>
	      </li>
	      <li><a href="/mpg/xcyt/data/NKTData.tar.gz">        
	          Download: Sample iNKT cell dataset (20
	    samples)</a><br/>
	      </li>
	      <li><a href="/mpg/xcyt/code/Sample.XCyt.Commands.R.gz">
	         Download: Sample R scripts for CD4+ T cell and iNKT cell dataset analysis</a><br/>
	      </li>
	      <li><a href="/mpg/xcyt/userinput/SampleInput.tar.gz">
	         Download: Sample User-input files for CD4+ T cell and
	         iNKT cell dataset analyses</a><br/>
	      </li>

         <p></p>
	      <li><a href="/mpg/xcyt/xcyt_manual.html">
		  Manual: X-Cyt </a></li>
		 
	    </ul>
<p></p>

<h2>Reference</h2>

<p></p>

<p></p>



<h2>Any questions?</h2>
<p>You can contact us at xinlihu AT broadinstitute DOT org</p>

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