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| <title>SHARPR</title> | ||
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| <body> | ||
| <div id="container" > | ||
| <div id="header"> | ||
| <h1><center>SHARPR (Systematic High-resolution Activation and Repression Profiling with Reporter-tiling)</center></h1> | ||
| <center> | ||
| <img src="sharprtiling.png"> | ||
| </center> | ||
| <center> | ||
| SHARPR is software for analyzing Massively Parallel Reporter Assay tiling designs allowing mapping | ||
| at high resolution activating and repressive nucleotides across thousands of regulatory regions. | ||
| </center> | ||
| <ul> | ||
| <li><a href="MPRAtiling/index.html">Interactive browser of all tiled regions from Ernst et al 2016</a> | ||
| <li><a href="SHARPR.zip">SHARPR software</a> (v1.0.2; <a href="versionlog.txt">version log</a>)<br> | ||
| <li><a href="SHARPR_manual.pdf">SHARPR manual</a><br> | ||
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| <li> Quick instructions on running SHARPR on example data:<br> | ||
| 1. Install Java 1.6 or later if not already installed.<br> | ||
| 2. Unzip the file SHARPR.zip.<br> | ||
| 3. | ||
| To run SHARPR on the sample data to infer base level predictions directly from count data type from the SHARPR directory:<br> | ||
| <font face="courier new"> | ||
| java -mx2000M -jar SHARPR.jar ExecuteAll EXAMPLE/HepG2_ScaleUpDesign1_minP_mRNA_Rep1.counts,EXAMPLE/HepG2_ScaleUpDesign1_minP_mRNA_Rep2.counts | ||
| EXAMPLE/ScaleUpDesign1_minP_Plasmid.counts,EXAMPLE/ScaleUpDesign1_minP_Plasmid.counts 3 145 5 31 EXAMPLE/basepredictions_HepG2_ScaleUpDesign1_minP.txt</font><br> | ||
| <li> SHARPR is described in:<br> | ||
| Ernst J#, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen T, Kellis M#.<br> | ||
| <a href="http://www.nature.com/nbt/journal/v34/n11/full/nbt.3678.html"> | ||
| Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions</a>.<br> | ||
| <i>Nature Biotechnology</i>, 34:1180-1190, 2016.<br> | ||
| <li> Files specific to the Ernst et al manuscript: | ||
| <ul> | ||
| <li> <a href="Pilot_counts_sequences.zip">Pilot (LargeStep) Raw Counts and Design Files</a> | ||
| <li> <a href="Pilot_normalized.zip">Pilot (LargeStep) Normalized Data Tables</a> | ||
| <li> <a href="Scaleup_counts_sequences.zip">Scale-up (SmallStep) Raw Counts and Design Files</a> | ||
| <li> Scale-up (SmallStep) Sharpr-MPRA Regulatory Activity Scores: <a href="HEPG2_SHARPR-MPRA_scores.zip">HepG2</a> and <a href="K562_SHARPR-MPRA_scores.zip">K562</a> | ||
| <li> Scale-up (SmallStep) Browser Files (BigWig - hg19): <a href="browser_combinedP_HEPG2.bw">HepG2 combinedP</a>, <a href="browser_combinedP_K562.bw">K562 combinedP</a>, | ||
| <a href="browser_minP_HEPG2.bw">HepG2 minP</a>, <a href="browser_minP_K562.bw">K562 minP</a>, | ||
| <a href="browser_SV40P_HEPG2.bw">HepG2 SV40P</a>, <a href="browser_SV40P_K562.bw">K562 SV40P</a> | ||
| <li> Scale-up (SmallStep) Image Files: <a href="images_HEPG2.tar.gz">HepG2 Images</a>, <a href="images_K562.tar.gz">K562 Images</a> | ||
| <li> <a href=" http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71279">Data in GEO</a> | ||
| </ul> | ||
| <br> | ||
| <li> Subscribe to a <a href="https://groups.google.com/forum/#!forum/sharpr-announce">mailing for announcements of new versions of SHARPR</a> | ||
| <li> <a href="https://github.com/jernst98/SHARPR">SHARPR source code on GitHub</a>. SHARPR makes | ||
| use of <a href="http://commons.apache.org/proper/commons-math/">The Apache Commons Mathematics Library (v3.3)</a>. | ||
| <li> <font size=1>Funding for SHARPR provided by NIH grants R01ES024995, U01HG007912 and U01MH105578 (J.E.), R01HG006785 (T.S.M.), R01GM113708, U01HG007610, R01HG004037, U54HG006991 and U41HG007000 (M.K.), an NSF CAREER Award #1254200, and an Alfred P. Sloan Fellowship (J.E.).</font? | ||
| </ul> | ||
| </font> | ||
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| </body> | ||
| </html> | ||
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