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figure_2_a_b.html
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<!DOCTYPE html>
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<div id="TOC">
<ul>
<li><a href="#figure-2">Figure 2</a><ul>
<li><a href="#overview">Overview</a></li>
<li><a href="#figure-2a">Figure 2A</a></li>
<li><a href="#figure-2b">Figure 2B</a></li>
<li><a href="#session-information">Session information</a></li>
</ul></li>
</ul>
</div>
<div id="figure-2" class="section level1">
<h1>Figure 2</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, 03:09 PM</p>
<div id="overview" class="section level2">
<h2>Overview</h2>
<p>MACS v2 was run on ChIP-nexus samples with these settings: <code>--keep-dup=all --call-summits</code> and <code>-g dm</code> or <code>-g hg</code>, depending on species.</p>
</div>
<div id="figure-2a" class="section level2">
<h2>Figure 2A</h2>
<p><img src="figure_2_a_b_output/tbp_and_dorsal_chipnexus_vs_chipnexus-1.png" title="" alt="" width="672" /><img src="figure_2_a_b_output/tbp_and_dorsal_chipnexus_vs_chipnexus-2.png" title="" alt="" width="672" /></p>
</div>
<div id="figure-2b" class="section level2">
<h2>Figure 2B</h2>
<p><img src="figure_2_a_b_output/tbp_and_dorsal_chipseq_vs_chipnexus-1.png" title="" alt="" width="672" /><img src="figure_2_a_b_output/tbp_and_dorsal_chipseq_vs_chipnexus-2.png" title="" alt="" width="672" /><img src="figure_2_a_b_output/tbp_and_dorsal_chipseq_vs_chipnexus-3.png" title="" alt="" width="672" /></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] grid stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] digest_0.6.4 yaml_2.1.13
[3] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome.Dmelanogaster.UCSC.dm3_1.4.0
[5] BSgenome_1.34.0 rtracklayer_1.26.1
[7] Biostrings_2.34.0 XVector_0.6.0
[9] GenomicRanges_1.18.1 GenomeInfoDb_1.2.0
[11] IRanges_2.0.0 S4Vectors_0.4.0
[13] BiocGenerics_0.12.0 ggplot2_1.0.0
[15] magrittr_1.0.1 xtable_1.7-4
loaded via a namespace (and not attached):
[1] base64enc_0.1-2 BatchJobs_1.4 BBmisc_1.7
[4] BiocParallel_1.0.0 bitops_1.0-6 brew_1.0-6
[7] checkmate_1.5.0 codetools_0.2-9 colorspace_1.2-4
[10] DBI_0.3.1 evaluate_0.5.5 fail_1.2
[13] foreach_1.4.2 formatR_1.0 GenomicAlignments_1.2.0
[16] gtable_0.1.2 htmltools_0.2.6 iterators_1.0.7
[19] knitr_1.7 MASS_7.3-35 munsell_0.4.2
[22] plyr_1.8.1 proto_0.3-10 Rcpp_0.11.3
[25] RCurl_1.95-4.3 reshape2_1.4 rmarkdown_0.3.3
[28] Rsamtools_1.18.0 RSQLite_0.11.4 scales_0.2.4
[31] sendmailR_1.2-1 stringr_0.6.2 tools_3.1.1
[34] XML_3.98-1.1 zlibbioc_1.12.0 </code></pre>
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