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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<title></title>
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}
</style>
<div class="container-fluid main-container">
<div id="TOC">
<ul>
<li><a href="#figure-1-tbp-dorsal-and-twist-examples">Figure 1: TBP, Dorsal and Twist examples</a><ul>
<li><a href="#overview">Overview</a></li>
<li><a href="#dorsal-embryos">Dorsal (embryos)</a></li>
<li><a href="#twist-embryos">Twist (embryos)</a></li>
<li><a href="#tbp-human">TBP (human)</a></li>
<li><a href="#session-information">Session information</a></li>
</ul></li>
</ul>
</div>
<div id="figure-1-tbp-dorsal-and-twist-examples" class="section level1">
<h1>Figure 1: TBP, Dorsal and Twist examples</h1>
<p><strong>Project:</strong> ChIP-nexus methods paper</p>
<p><strong>Author:</strong> <a href="mailto:jjj@stowers.org">Jeff Johnston</a></p>
<p><strong>Generated:</strong> Thu Dec 04 2014, 02:59 PM</p>
<div id="overview" class="section level2">
<h2>Overview</h2>
<p>Examples of TBP, Dorsal and Twist binding at single regions</p>
<!-- html table generated in R 3.1.1 by xtable 1.7-4 package -->
<!-- Thu Dec 4 14:59:11 2014 -->
<table border="1">
<tr>
<th>
chr
</th>
<th>
start
</th>
<th>
end
</th>
<th>
name
</th>
<th>
factor
</th>
<th>
figure
</th>
</tr>
<tr>
<td>
chr2L
</td>
<td align="right">
2456425
</td>
<td align="right">
2456724
</td>
<td>
dpp repressor
</td>
<td>
dl
</td>
<td>
2
</td>
</tr>
<tr>
<td>
chr3L
</td>
<td align="right">
1461814
</td>
<td align="right">
1462133
</td>
<td>
rho enhancer
</td>
<td>
dl
</td>
<td>
2
</td>
</tr>
<tr>
<td>
chr6
</td>
<td align="right">
133135498
</td>
<td align="right">
133135797
</td>
<td>
RPS12 promoter
</td>
<td>
tbp
</td>
<td>
2
</td>
</tr>
<tr>
<td>
chr3L
</td>
<td align="right">
1461814
</td>
<td align="right">
1462133
</td>
<td>
rho enhancer
</td>
<td>
twi
</td>
<td>
2
</td>
</tr>
</table>
</div>
<div id="dorsal-embryos" class="section level2">
<h2>Dorsal (embryos)</h2>
<p><img src="figure_1_example_regions_output/dl_examples-1.png" title="" alt="" width="864" /><img src="figure_1_example_regions_output/dl_examples-2.png" title="" alt="" width="864" /><img src="figure_1_example_regions_output/dl_examples-3.png" title="" alt="" width="864" /><img src="figure_1_example_regions_output/dl_examples-4.png" title="" alt="" width="864" /></p>
</div>
<div id="twist-embryos" class="section level2">
<h2>Twist (embryos)</h2>
<p><img src="figure_1_example_regions_output/twi_examples-1.png" title="" alt="" width="864" /></p>
</div>
<div id="tbp-human" class="section level2">
<h2>TBP (human)</h2>
<p><img src="figure_1_example_regions_output/tbp_examples-1.png" title="" alt="" width="864" /></p>
</div>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<p>For reproducibility, this analysis was performed with the following R/Bioconductor session:</p>
<pre><code>R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel grid stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] digest_0.6.4
[2] yaml_2.1.13
[3] BSgenome.Dmelanogaster.UCSC.dm3_1.4.0
[4] BSgenome_1.34.0
[5] rtracklayer_1.26.1
[6] Biostrings_2.34.0
[7] XVector_0.6.0
[8] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.0.0
[9] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0
[10] GenomicFeatures_1.18.1
[11] AnnotationDbi_1.28.0
[12] Biobase_2.26.0
[13] Gviz_1.10.0
[14] GenomicRanges_1.18.1
[15] GenomeInfoDb_1.2.0
[16] IRanges_2.0.0
[17] S4Vectors_0.4.0
[18] BiocGenerics_0.12.0
[19] xtable_1.7-4
loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 base64enc_0.1-2 BatchJobs_1.4
[4] BBmisc_1.7 BiocParallel_1.0.0 biomaRt_2.22.0
[7] biovizBase_1.14.0 bitops_1.0-6 brew_1.0-6
[10] checkmate_1.5.0 cluster_1.15.3 codetools_0.2-9
[13] colorspace_1.2-4 DBI_0.3.1 dichromat_2.0-0
[16] evaluate_0.5.5 fail_1.2 foreach_1.4.2
[19] foreign_0.8-61 formatR_1.0 Formula_1.1-2
[22] GenomicAlignments_1.2.0 Hmisc_3.14-5 htmltools_0.2.6
[25] iterators_1.0.7 knitr_1.7 lattice_0.20-29
[28] latticeExtra_0.6-26 matrixStats_0.10.3 munsell_0.4.2
[31] nnet_7.3-8 plyr_1.8.1 RColorBrewer_1.0-5
[34] Rcpp_0.11.3 RCurl_1.95-4.3 rmarkdown_0.3.3
[37] R.methodsS3_1.6.1 rpart_4.1-8 Rsamtools_1.18.0
[40] RSQLite_0.11.4 scales_0.2.4 sendmailR_1.2-1
[43] splines_3.1.1 stringr_0.6.2 survival_2.37-7
[46] tools_3.1.1 VariantAnnotation_1.12.1 XML_3.98-1.1
[49] zlibbioc_1.12.0 </code></pre>
</div>
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