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20 changes: 10 additions & 10 deletions index.Rmd
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Expand Up @@ -55,11 +55,11 @@ This section of the website describes the code and reports associated with the h
There are 9 main `bash` scripts named _step1-*_ through _step9-*_.

1. _fullCoverage_ loads the data from the raw files. See [step1-fullCoverage.sh](step1-fullCoverage.sh) and [step1-fullCoverage.R](step1-fullCoverage.R).
1. _makeModels_ creates the models used for the single-level base analysis. See [step2-makeModels.sh](step2-makeModels.sh) and [step2-makeModels.R](step2-makeModels.R).
1. _analyzeChr_ runs the single-base level analysis by chromosome. See [step3-analyzeChr.sh](step3-analyzeChr.sh) and [step3-analyzeChr.R](step3-analyzeChr.R).
1. _mergeResults_ merges the single-base level analysis results for all the chromosomes. See [step4-mergeResults.sh](step4-mergeResults.sh).
1. _derfinderReport_ generates a HTML report for the single-base level DERs. See [step5-derfinderReport.sh](step5-derfinderReport.sh).
1. _regionMatrix_ identifies the expressed regions for the expressed-regions level approach. See [step6-regionMatrix.sh](step6-regionMatrix.sh).
1. _makeModels_ creates the models used for the single base-level analysis. See [step2-makeModels.sh](step2-makeModels.sh) and [step2-makeModels.R](step2-makeModels.R).
1. _analyzeChr_ runs the single base-level analysis by chromosome. See [step3-analyzeChr.sh](step3-analyzeChr.sh) and [step3-analyzeChr.R](step3-analyzeChr.R).
1. _mergeResults_ merges the single base-level analysis results for all the chromosomes. See [step4-mergeResults.sh](step4-mergeResults.sh).
1. _derfinderReport_ generates a HTML report for the single base-level DERs. See [step5-derfinderReport.sh](step5-derfinderReport.sh).
1. _regionMatrix_ identifies the expressed regions for the expressed regions-level approach. See [step6-regionMatrix.sh](step6-regionMatrix.sh).
1. _regMatVsDERs_ creates a simple HTML report comparing the single-base and expressed-regions approaches. See [step7-regMatVsDERs.sh](step7-regMatVsDERs.sh) and [step7-regMatVsDERs.Rmd](step7-regMatVsDERs.Rmd).
1. _coverageToExon_ creates an exon count table using known annotation information. See [step8-coverageToExon.sh](step8-coverageToExon.sh) and [step8-coverageToExon.R](step8-coverageToExon.R).
1. _summaryInfo_ creates a HTML report with brief summary information for the given experiment. See [step9-summaryInfo.sh](step9-summaryInfo.sh), [step9-summaryInfo.R](step9-summaryInfo.R), and [step9-summaryInfo.Rmd](step9-summaryInfo.Rmd).
Expand All @@ -81,13 +81,13 @@ The [check-analysis-time.R](check-analysis-time.R) script was useful for checkin



We expect that these scripts will be useful to `derfinder` users who want to automate the single-base level and/or expressed-regions level analyses for several data sets and/or have the jobs run automatically without having to check if each step has finished running.
We expect that these scripts will be useful to `derfinder` users who want to automate the single base-level and/or expressed regions-level analyses for several data sets and/or have the jobs run automatically without having to check if each step has finished running.


Note that all `bash` scripts are tailored for the cluster we have access to which administer job queues with Sun Grid Engine (SGE).


## Single-base level
## Single base-level

### Quick overview HTML report

Expand All @@ -97,13 +97,13 @@ This HTML report contains basic information on the `derfinder` `r citep(bib[["de
* What is the number of candidate regions?
* How many candidate regions are significant?

It also illustrates three clusters of candidate differentially expressed regions (DERs) from the single-base level analysis. You can view the report by following this link:
It also illustrates three clusters of candidate differentially expressed regions (DERs) from the single base-level analysis. You can view the report by following this link:

* [Hippo](hippo/summaryInfo/run3-v1.0.10/summaryInfo.html)

### CSV files and annotation comparison

This HTML report has the code for loading the R data files and generating the CSV files. The report also has Venn diagrams showing the number of candidate DERs from the single-base level analysis that overlap known exons, introns and intergenic regions using the UCSC hg19 annotation. It also includes a detailed description of the columns in the CSV files.
This HTML report has the code for loading the R data files and generating the CSV files. The report also has Venn diagrams showing the number of candidate DERs from the single base-level analysis that overlap known exons, introns and intergenic regions using the UCSC hg19 annotation. It also includes a detailed description of the columns in the CSV files.

View the [venn](venn/venn.html) report or its `R Markdown` source file [venn.Rmd](venn/venn.Rmd).

Expand All @@ -118,7 +118,7 @@ View the [timing](timing/timing.html) report or check the `R Markdown` file [tim

# Hippo vs previous results

[compareVsPNAS](hippo/pnas/compareVsPNAS.html) is an HTML report comparing 29 regions that were previously found to be differentially expressed `r citep(bib[["zhou2011"]])` versus the `derfinder` single-base level results. It also has code for identified differentially expressed disjoint exons. The additional script [counts-gene.R](hippo/counts-gene/counts-gene.R) has the code for gene counting with `summarizeOverlaps()`. [compareVsPNAS-gene](hippo/pnas/compareVsPNAS-gene.html) compares the results between `DESeq2` and `edgeR`-robust against `derfinder` at the gene level with 40 total plots: 10 for each case of agreement/disagreement.
[compareVsPNAS](hippo/pnas/compareVsPNAS.html) is an HTML report comparing 29 regions that were previously found to be differentially expressed `r citep(bib[["zhou2011"]])` versus the `derfinder` single base-level results. It also has code for identified differentially expressed disjoint exons. The additional script [counts-gene.R](hippo/counts-gene/counts-gene.R) has the code for gene counting with `summarizeOverlaps()`. [compareVsPNAS-gene](hippo/pnas/compareVsPNAS-gene.html) compares the results between `DESeq2` and `edgeR`-robust against `derfinder` at the gene level with 40 total plots: 10 for each case of agreement/disagreement.

View the [compareVsPNAS](hippo/pnas/compareVsPNAS.html) report or check the `R Markdown` file [compareVsPNAS.Rmd](hippo/pnas/compareVsPNAS.Rmd) run by the [runComparison.sh](hippo/pnas/runComparison.sh) script. Also view the [compareVsPNAS-gene](hippo/pnas/compareVsPNAS-gene.html) report and its linked `R Markdown` file [compareVsPNAS-gene.Rmd](hippo/pnas/compareVsPNAS-gene.Rmd).

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34 changes: 17 additions & 17 deletions index.html
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Expand Up @@ -10,7 +10,7 @@

<meta name="author" content="L Collado-Torres" />

<meta name="date" content="2016-02-20" />
<meta name="date" content="2016-03-21" />

<title>derfinder counting paper Supplementary Website</title>

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<div id="header">
<h1 class="title">derfinder counting paper Supplementary Website</h1>
<h4 class="author"><em>L Collado-Torres</em></h4>
<h4 class="date"><em>20 February 2016</em></h4>
<h4 class="date"><em>21 March 2016</em></h4>
</div>

<h1>Contents</h1>
<div id="TOC">
<ul>
<li><a href="#hippocampus-and-time-course-data-sets"><span class="toc-section-number">1</span> Hippocampus and time-course data sets</a><ul>
<li><a href="#code-to-reproduce-analyses"><span class="toc-section-number">1.1</span> Code to reproduce analyses</a></li>
<li><a href="#single-base-level"><span class="toc-section-number">1.2</span> Single-base level</a><ul>
<li><a href="#single-base-level"><span class="toc-section-number">1.2</span> Single base-level</a><ul>
<li><a href="#quick-overview-html-report"><span class="toc-section-number">1.2.1</span> Quick overview HTML report</a></li>
<li><a href="#csv-files-and-annotation-comparison"><span class="toc-section-number">1.2.2</span> CSV files and annotation comparison</a></li>
</ul></li>
Expand All @@ -81,11 +81,11 @@ <h2><span class="header-section-number">1.1</span> Code to reproduce analyses</h
<p>There are 9 main <code>bash</code> scripts named _step1-*_ through _step9-*_.</p>
<ol style="list-style-type: decimal">
<li><em>fullCoverage</em> loads the data from the raw files. See <a href="step1-fullCoverage.sh" class="uri">step1-fullCoverage.sh</a> and <a href="step1-fullCoverage.R" class="uri">step1-fullCoverage.R</a>.</li>
<li><em>makeModels</em> creates the models used for the single-level base analysis. See <a href="step2-makeModels.sh" class="uri">step2-makeModels.sh</a> and <a href="step2-makeModels.R" class="uri">step2-makeModels.R</a>.</li>
<li><em>analyzeChr</em> runs the single-base level analysis by chromosome. See <a href="step3-analyzeChr.sh" class="uri">step3-analyzeChr.sh</a> and <a href="step3-analyzeChr.R" class="uri">step3-analyzeChr.R</a>.</li>
<li><em>mergeResults</em> merges the single-base level analysis results for all the chromosomes. See <a href="step4-mergeResults.sh" class="uri">step4-mergeResults.sh</a>.</li>
<li><em>derfinderReport</em> generates a HTML report for the single-base level DERs. See <a href="step5-derfinderReport.sh" class="uri">step5-derfinderReport.sh</a>.</li>
<li><em>regionMatrix</em> identifies the expressed regions for the expressed-regions level approach. See <a href="step6-regionMatrix.sh" class="uri">step6-regionMatrix.sh</a>.</li>
<li><em>makeModels</em> creates the models used for the single base-level analysis. See <a href="step2-makeModels.sh" class="uri">step2-makeModels.sh</a> and <a href="step2-makeModels.R" class="uri">step2-makeModels.R</a>.</li>
<li><em>analyzeChr</em> runs the single base-level analysis by chromosome. See <a href="step3-analyzeChr.sh" class="uri">step3-analyzeChr.sh</a> and <a href="step3-analyzeChr.R" class="uri">step3-analyzeChr.R</a>.</li>
<li><em>mergeResults</em> merges the single base-level analysis results for all the chromosomes. See <a href="step4-mergeResults.sh" class="uri">step4-mergeResults.sh</a>.</li>
<li><em>derfinderReport</em> generates a HTML report for the single base-level DERs. See <a href="step5-derfinderReport.sh" class="uri">step5-derfinderReport.sh</a>.</li>
<li><em>regionMatrix</em> identifies the expressed regions for the expressed regions-level approach. See <a href="step6-regionMatrix.sh" class="uri">step6-regionMatrix.sh</a>.</li>
<li><em>regMatVsDERs</em> creates a simple HTML report comparing the single-base and expressed-regions approaches. See <a href="step7-regMatVsDERs.sh" class="uri">step7-regMatVsDERs.sh</a> and <a href="step7-regMatVsDERs.Rmd" class="uri">step7-regMatVsDERs.Rmd</a>.</li>
<li><em>coverageToExon</em> creates an exon count table using known annotation information. See <a href="step8-coverageToExon.sh" class="uri">step8-coverageToExon.sh</a> and <a href="step8-coverageToExon.R" class="uri">step8-coverageToExon.R</a>.</li>
<li><em>summaryInfo</em> creates a HTML report with brief summary information for the given experiment. See <a href="step9-summaryInfo.sh" class="uri">step9-summaryInfo.sh</a>, <a href="step9-summaryInfo.R" class="uri">step9-summaryInfo.R</a>, and <a href="step9-summaryInfo.Rmd" class="uri">step9-summaryInfo.Rmd</a>.</li>
Expand All @@ -100,11 +100,11 @@ <h2><span class="header-section-number">1.1</span> Code to reproduce analyses</h
<p>A final <code>bash</code> script, <a href="run-all.sh" class="uri">run-all.sh</a>, can be used to run the main 9 steps (or a subset of them).</p>
<p>All scripts show at the beginning the way they were used. Some of them generate intermediate small <code>bash</code> scripts, for example one script per chromosome for the <em>analyzeChr</em> step. For some steps, there is a companion <code>R</code> or <code>R Markdown</code> code file when the code is more involved or an HTML file is generated in the particular step.</p>
<p>The <a href="check-analysis-time.R" class="uri">check-analysis-time.R</a> script was useful for checking the progress of the <em>step3-analyzeChr</em> jobs and detect whenever a node in the cluster was presenting problems.</p>
<p>We expect that these scripts will be useful to <code>derfinder</code> users who want to automate the single-base level and/or expressed-regions level analyses for several data sets and/or have the jobs run automatically without having to check if each step has finished running.</p>
<p>We expect that these scripts will be useful to <code>derfinder</code> users who want to automate the single base-level and/or expressed regions-level analyses for several data sets and/or have the jobs run automatically without having to check if each step has finished running.</p>
<p>Note that all <code>bash</code> scripts are tailored for the cluster we have access to which administer job queues with Sun Grid Engine (SGE).</p>
</div>
<div id="single-base-level" class="section level2">
<h2><span class="header-section-number">1.2</span> Single-base level</h2>
<h2><span class="header-section-number">1.2</span> Single base-level</h2>
<div id="quick-overview-html-report" class="section level3">
<h3><span class="header-section-number">1.2.1</span> Quick overview HTML report</h3>
<p>This HTML report contains basic information on the <code>derfinder</code> <a id="cite-derfinder"></a>(<a href="http://www.biorxiv.org/content/early/2015/02/19/015370.abstract">Collado-Torres, Frazee, Love, Irizarry, et al., 2015</a>) results from the <em>Hippo</em> data set. The report answers basic questions such as:</p>
Expand All @@ -113,14 +113,14 @@ <h3><span class="header-section-number">1.2.1</span> Quick overview HTML report<
<li>What is the number of candidate regions?</li>
<li>How many candidate regions are significant?</li>
</ul>
<p>It also illustrates three clusters of candidate differentially expressed regions (DERs) from the single-base level analysis. You can view the report by following this link:</p>
<p>It also illustrates three clusters of candidate differentially expressed regions (DERs) from the single base-level analysis. You can view the report by following this link:</p>
<ul>
<li><a href="hippo/summaryInfo/run3-v1.0.10/summaryInfo.html">Hippo</a></li>
</ul>
</div>
<div id="csv-files-and-annotation-comparison" class="section level3">
<h3><span class="header-section-number">1.2.2</span> CSV files and annotation comparison</h3>
<p>This HTML report has the code for loading the R data files and generating the CSV files. The report also has Venn diagrams showing the number of candidate DERs from the single-base level analysis that overlap known exons, introns and intergenic regions using the UCSC hg19 annotation. It also includes a detailed description of the columns in the CSV files.</p>
<p>This HTML report has the code for loading the R data files and generating the CSV files. The report also has Venn diagrams showing the number of candidate DERs from the single base-level analysis that overlap known exons, introns and intergenic regions using the UCSC hg19 annotation. It also includes a detailed description of the columns in the CSV files.</p>
<p>View the <a href="venn/venn.html">venn</a> report or its <code>R Markdown</code> source file <a href="venn/venn.Rmd">venn.Rmd</a>.</p>
</div>
</div>
Expand All @@ -132,7 +132,7 @@ <h2><span class="header-section-number">1.3</span> Timing and memory information
</div>
<div id="hippo-vs-previous-results" class="section level1">
<h1><span class="header-section-number">2</span> Hippo vs previous results</h1>
<p><a href="hippo/pnas/compareVsPNAS.html">compareVsPNAS</a> is an HTML report comparing 29 regions that were previously found to be differentially expressed <a id="cite-zhou2011"></a>(<a href="#bib-zhou2011">Zhou, Zhifeng, Yuan, Qiaoping, et al., 2011</a>) versus the <code>derfinder</code> single-base level results. It also has code for identified differentially expressed disjoint exons. The additional script <a href="hippo/counts-gene/counts-gene.R">counts-gene.R</a> has the code for gene counting with <code>summarizeOverlaps()</code>. <a href="hippo/pnas/compareVsPNAS-gene.html">compareVsPNAS-gene</a> compares the results between <code>DESeq2</code> and <code>edgeR</code>-robust against <code>derfinder</code> at the gene level with 40 total plots: 10 for each case of agreement/disagreement.</p>
<p><a href="hippo/pnas/compareVsPNAS.html">compareVsPNAS</a> is an HTML report comparing 29 regions that were previously found to be differentially expressed <a id="cite-zhou2011"></a>(<a href="#bib-zhou2011">Zhou, Zhifeng, Yuan, Qiaoping, et al., 2011</a>) versus the <code>derfinder</code> single base-level results. It also has code for identified differentially expressed disjoint exons. The additional script <a href="hippo/counts-gene/counts-gene.R">counts-gene.R</a> has the code for gene counting with <code>summarizeOverlaps()</code>. <a href="hippo/pnas/compareVsPNAS-gene.html">compareVsPNAS-gene</a> compares the results between <code>DESeq2</code> and <code>edgeR</code>-robust against <code>derfinder</code> at the gene level with 40 total plots: 10 for each case of agreement/disagreement.</p>
<p>View the <a href="hippo/pnas/compareVsPNAS.html">compareVsPNAS</a> report or check the <code>R Markdown</code> file <a href="hippo/pnas/compareVsPNAS.Rmd">compareVsPNAS.Rmd</a> run by the <a href="hippo/pnas/runComparison.sh">runComparison.sh</a> script. Also view the <a href="hippo/pnas/compareVsPNAS-gene.html">compareVsPNAS-gene</a> report and its linked <code>R Markdown</code> file <a href="hippo/pnas/compareVsPNAS-gene.Rmd">compareVsPNAS-gene.Rmd</a>.</p>
</div>
<div id="additional-analyses" class="section level1">
Expand All @@ -147,9 +147,9 @@ <h1><span class="header-section-number">3</span> Additional analyses</h1>
<div id="reproducibility" class="section level1">
<h1><span class="header-section-number">4</span> Reproducibility</h1>
<p>Date this page was generated.</p>
<pre><code>## [1] &quot;2016-02-20 11:02:47 EST&quot;</code></pre>
<pre><code>## [1] &quot;2016-03-21 10:16:26 EDT&quot;</code></pre>
<p>Wallclock time spent generating the report.</p>
<pre><code>## Time difference of 1.252 secs</code></pre>
<pre><code>## Time difference of 1.172 secs</code></pre>
<p><code>R</code> session information.</p>
<pre><code>## Session info -----------------------------------------------------------------------------------------------------------</code></pre>
<pre><code>## setting value
Expand All @@ -159,7 +159,7 @@ <h1><span class="header-section-number">4</span> Reproducibility</h1>
## language (EN)
## collate en_US.UTF-8
## tz America/New_York
## date 2016-02-20</code></pre>
## date 2016-03-21</code></pre>
<pre><code>## Packages ---------------------------------------------------------------------------------------------------------------</code></pre>
<pre><code>## package * version date source
## bibtex 0.4.0 2014-12-31 CRAN (R 3.2.0)
Expand All @@ -180,7 +180,7 @@ <h1><span class="header-section-number">4</span> Reproducibility</h1>
## R6 2.1.2 2016-01-26 CRAN (R 3.2.3)
## Rcpp 0.12.3 2016-01-10 CRAN (R 3.2.3)
## RCurl 1.95-4.7 2015-06-30 CRAN (R 3.2.1)
## RefManageR 0.10.5 2016-01-02 CRAN (R 3.2.3)
## RefManageR 0.10.6 2016-02-15 CRAN (R 3.2.3)
## RJSONIO 1.3-0 2014-07-28 CRAN (R 3.2.0)
## rmarkdown * 0.9.2 2016-01-01 CRAN (R 3.2.3)
## stringi 1.0-1 2015-10-22 CRAN (R 3.2.0)
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