ÿþ<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <meta http-equiv="content-type" content="text/html; charset=iso-8859-1" /> <link rel="stylesheet" type="text/css" href="style.css"> <title>Software/Programs</title> </head> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml"> <body bgcolor="#EBF4EA"> <table > <tr> <th align="center" height="56" width="100%" colspan="9"><B><FONT face="Garamond" size="+3"><FONT size="0"><FONT size="+2" color="#002f5e" face="Garamond">Yasui Biostatistics Research Team</FONT></FONT></FONT></B>&nbsp;&nbsp;&nbsp;</th> </tr> <tr> <td align="center" width="200" height="22"><p><font color="#008000"><font face="Garamond"><font size="7"><font size="2"><font size="3"></font></font></font></font></font></p></td> <td align="center" width="201" height="22"><p><A href="homepage.html"><FONT face="Garamond">Home</font></A></p></td> <td align="center" width="201" height="22"><p><A href="yutaka from PHS.html"><FONT face="Garamond">Yutaka Yasui</font></A></p></td> <td align="center" width="201" height="22"><p><A href="Yutaka's Team members.htm"><FONT face="Garamond">Team Members</font></A></p></td> <td align="center" width="201" height="22"><p><A href="Research.html"><FONT face="Garamond">Research</font></A></p></td> <td align="center" width="201" height="22"><p><A href="publications.html"><FONT face="Garamond">Publications</font></A></p></td> <td align="center" width="201" height="22"><p><A href="software.html"><FONT face="Garamond">Software/Programs</font></A></p></td> <td align="center" width="200" height="22"><p><font color="#008000"><font face="Garamond"><font size="7"><font size="2"><font size="3"></font></font></font></font></font></p></td> </tr> </table> <br> <br> <blockquote> <h3><font size="4"><b><font color="#002f5e" face="Garamond">Software/Programs</font></b></font></h3> <tr> <td width="100" height="22"><p><font color="#008000"><font face="Garamond"><font size="7"><font size="2"><font size="3"></font></font></font></font></font></p></td> <td width="201" height="22"><p><font color="#008000" size="3" face="Garamond"><a href="#SAM-GS" tabindex="2">SAM-GS (Dinu et al., 2007)</a></font></p></td> <td width="201" height="22"><p><font color="#008000" size="3" face="Garamond"><a href="#SAM-GSR" tabindex="2">SAM-GSR</a></font></p></td> <td width="201" height="22"><p><font color="#008000" size="3" face="Garamond"><a href="#PBEE" tabindex="1" hspace="2" vspace="1">PBEE (Martinez et al., 2007)</a></font></p></td> </tr> &nbsp; </blockquote> <font face="Garamond"> <blockquote> <hr> <center><h2> <font color="#002f5e"> <a name="SAM-GS">SAM-GS: Significant Analysis of Microarrays for Gene Sets</a></font></h2></center> <center><blockquote><h3> Gene Set Analysis Software</h3></blockquote></center> <h4> " Paper: </h4> <blockquote> Irina Dinu, John D. Potter, Thomas Mueller, Qi Liu, Adeniyi J. Adewale, Gian S. Jhangri, Gunilla Einecke, Konrad S. Famulski, Philip Halloran, and Yutaka Yasui, <a href="http://biostats.bepress.com/cobra/ps/art16" target="_blank"> "Improving GSEA for Analysis of Biologic Pathways for Differential Gene Expression across a Binary Phenotype " </a>&nbsp; (January 2007). COBRA Preprint Series. Article 16. <br> <br> Dinu I, Potter JD, Mueller T, Liu Q, Adewale AJ, Jhangri GS, Einecke G, Famulski KS, Halloran P, and Yasui Y. <a href="http://www.biomedcentral.com/1471-2105/8/242" target="_blank">"Improving Gene Set Analysis of Microarray Data by SAM-GS"</a>, BMC Bioinformatics 2007, 8:242 <br> <br> Liu Q, Dinu I, Adewale AJ, Potter JD, and Yasui Y. <a href="http://www.biomedcentral.com/1471-2105/8/431" target="_blank">"Comparative Evaluation of Gene-set Analysis Methods"</a>, BMC Bioinformatics 2007, 8:431 </blockquote> <h4> " Software: </h4> <blockquote> <p>To obtain the software (SAM-GS version 1.0.2 made available on <b><u>May 28, 2007</u></b>), please go to the <a href="http://www.sam-gs.org/" target="_blank"> registration page</a>. <p>SAM-GS was created with R, downloadable from <a href="http://cran.r-project.org/" target="_blank">http://cran.r-project.org/.</a></p> <p><a href="SAM-GS/SAMGS April 2011.r" target="_blank"><b><FONT size="+2" color="#E62B86" face="Garamond">R code of SAM-GS</font></b></a>&nbsp; (programmed by Irina Dinu, modified and improved by Dr. Aurelien de Reynies at Ligue Nationale Contre le Cancer, Paris. Dr. Aurelien de Reynies kindly revised the code and we reposted on April 4, 2011). <p><a href="http://acc.crs4.it/acdc/pygsa/" target="_blank"><b><FONT size="+2" color="#E62B86" face="Garamond">Python version of SAM-GS</font></b></a> (developed by Dr. Simone Leo at the Advanced Computing and Communications Program of CRS4, Italy). <p><a href="HLCT.R" target="_blank"><b><FONT size="+2" color="#E62B86" face="Garamond">R code of Linear Combination Test for Hierarchical Gene Set Analysis. </font></b></a>&nbsp; </blockquote> <h4> " Documentation of the software: </h4> <blockquote> <a href="SAM-GS/SAM-GS Documentation version 1.0.2.pdf" target="_blank">SAM-GS Documentation (version 1.0.2)</a>&nbsp; &nbsp;&nbsp;&nbsp; </blockquote> <h4> " Example datasets: </h4> <blockquote> <p>Gene-expression dataset: &nbsp; &nbsp; &nbsp; <a href="SAM-GS/p53.csv" target="_blank">p53.csv</a>&nbsp; &nbsp;&nbsp;&nbsp;</p> <p>Gene-set-definition dataset:&nbsp; <a href="SAM-GS/c2part1.csv" target="_blank">c2part1.csv</a>&nbsp;&nbsp;&nbsp;&nbsp;<a href="SAM-GS/c2part2.csv" target="_blank">c2part2.csv</a>&nbsp;&nbsp;&nbsp;&nbsp;<a href="SAM-GS/c2.v2.symbols.gmt" target="_blank">c2.v2.symbols.gmt</a></p> </blockquote> <br> <br> <br> <center><h2> <font color="#002f5e"> <a name="SAM-GSR">SAM-GSR: Significant Analysis of Microarrays for Gene Set <U><I>Reduction</I></U></a></font></h2></center> <h4> " Code</h4> <blockquote> <p><a href="code Bioinf.txt">R code of SAM-GSR</a>. (Please note this is not the R code of SAM-GS. Please see above for the R code of SAM-GS)</p> </blockquote> <br> <br> <br> <center><h2> <font color="#002f5e"> <a name="PBEE"> PBEE: Population Based Estimating Equation</a></font></h2></center> <center><blockquote><h3>Integrated Estimating Equations of Individual and Aggregated Health Data </h3></blockquote></center> <h4> " Paper: </h4> <blockquote> Jose Miguel Martinez, Joan Benach, Josep Ginebra, Fernando G. Benavides, and Yutaka Yasui (2007) <a href="http://www.bepress.com/ijb/vol3/iss1/10/" target="_blank"> "An Integrated Analysis of Individual and Aggregated Health Data Using Estimating Equations"</a>, The International Journal of Biostatistics: Vol. 3: Iss. 1, Article 10. </blockquote> <h4> " Three R programs used for the simulation work: </h4> <blockquote> <p> <a href="PBEE/ECC.txt" target="_blank">ECC.txt</a>&nbsp;&nbsp;&nbsp;&nbsp;<a href="PBEE/NCC.txt" target="_blank">NCC.txt</a>&nbsp;&nbsp;&nbsp;&nbsp;<a href="PBEE/SCC.txt" target="_blank">SCC.txt</a></p> </blockquote> </blockquote> </blockquote> </body> </html>