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supplementary1_compare_replicates.html
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<ul>
<li><a href="#supplementary-compare-replicates">Supplementary compare replicates</a><ul>
<li><a href="#scatter-plot">scatter plot</a></li>
<li><a href="#plot-single-gene-example">plot single gene example</a></li>
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<div id="supplementary-compare-replicates" class="section level1">
<h1>Supplementary compare replicates</h1>
<p><strong>Author:</strong> <a href="mailto:[email protected]">Wanqing Shao</a></p>
<p><strong>Generated:</strong> Fri Apr 07 2017, 07:21 PM</p>
<div id="scatter-plot" class="section level3">
<h3>scatter plot</h3>
<p>Scatter plot showing the consistency between replicates, Pol II and TFIIA at control condition are used as example</p>
<p><img src="supplementary1_compare_replicates/scatter_plot-1.png" width="672" /><img src="supplementary1_compare_replicates/scatter_plot-2.png" width="672" /></p>
</div>
<div id="plot-single-gene-example" class="section level3">
<h3>plot single gene example</h3>
<p>Plot Pol II and TFIIA signal at gene pino</p>
<p><img src="supplementary1_compare_replicates/single_gene-1.png" width="672" /><img src="supplementary1_compare_replicates/single_gene-2.png" width="672" /><img src="supplementary1_compare_replicates/single_gene-3.png" width="672" /><img src="supplementary1_compare_replicates/single_gene-4.png" width="672" /></p>
<pre><code>## R version 3.3.2 (2016-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.2 LTS
##
## 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 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] lattice_0.20-34 reshape2_1.4.2 rtracklayer_1.32.2
## [4] digest_0.6.12 pander_0.6.0 ggplot2_2.2.1
## [7] magrittr_1.5 GenomicRanges_1.24.3 GenomeInfoDb_1.8.7
## [10] IRanges_2.6.1 S4Vectors_0.10.3 BiocGenerics_0.18.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.9 plyr_1.8.4
## [3] XVector_0.12.1 bitops_1.0-6
## [5] tools_3.3.2 zlibbioc_1.18.0
## [7] evaluate_0.10 tibble_1.2
## [9] gtable_0.2.0 yaml_2.1.14
## [11] stringr_1.2.0 knitr_1.15.1
## [13] Biostrings_2.40.2 rprojroot_1.2
## [15] grid_3.3.2 Biobase_2.32.0
## [17] XML_3.98-1.5 BiocParallel_1.6.6
## [19] rmarkdown_1.3 backports_1.0.5
## [21] scales_0.4.1 Rsamtools_1.24.0
## [23] htmltools_0.3.5 GenomicAlignments_1.8.4
## [25] assertthat_0.1 SummarizedExperiment_1.2.3
## [27] colorspace_1.3-2 labeling_0.3
## [29] stringi_1.1.2 RCurl_1.95-4.8
## [31] lazyeval_0.2.0 munsell_0.4.3</code></pre>
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