Generate all index.html files

Snakefile

@@ -139,7 +139,7 @@ all_example_files = all_example_files.union(index_files)
 all_example_files = all_example_files.union(r_html_files)
 
 rule build_all:
-    input: 'ryan_thompson_resume.pdf', 'ryan_thompson_resume.html', index_files, r_html_files
+    input: 'ryan_thompson_resume.pdf', 'ryan_thompson_resume.html', 'index.html', index_files, r_html_files
 
 rule create_resume_pdf:
     input: lyxfile='ryan_thompson_resume.lyx',
@@ -165,9 +165,9 @@ rule link_resume_to_index_html:
     output: 'index.html'
     shell: 'ln -s {input:q} {output:q}'
 
-rule readme_to_index_html:
-    input: '{dirname}/README.mkdn'
-    output: '{dirname}/index.html'
+rule examples_readme_to_index_html:
+    input: '{dirname}README.mkdn'
+    output: '{dirname,examples(/.*)?/}index.html'
     shell: 'pandoc -t html -o {output[0]:q} {input[0]:q}'
 
 rule R_to_html:

examples/Gaasterland/index.html

@@ -0,0 +1,9 @@
+<ul>
+<li><a href="delox.R.html"><code>delox.R.html</code></a>: The R code for <a href="https://academic.oup.com/nar/article/40/3/e24/1128321/Illumina-mate-paired-DNA-sequencing-library">Deloxer</a></li>
+<li><a href="depth-consistency.pdf"><code>depth-consistency.pdf</code></a>: Visualization of consistency of coverage depth between 2 Exome sequencing replicates</li>
+<li><a href="illumina-qc.html"><code>illumina-qc.html</code></a>: QC chart indicating quality score dropoff along read length for exome sequencing data set.</li>
+<li><a href="ipi-results-small.txt"><code>ipi-results-small.txt</code></a>: A sample of output showing alignment of <em>de novo</em> assembled black rhino and white rhino transcript sequences to human proteins. This was used to find differences between the two rhino species in otherwise conserved regions.</li>
+<li><a href="mirna-results.html"><code>mirna-results.html</code></a>: Example output from miRNA binding site predictions</li>
+<li><a href="neartarget.pdf"><code>neartarget.pdf</code></a>: Visualization of mean coverage depth in exome sequencing data in the regions flanking the probe targets.</li>
+<li><a href="on-off-coverage.pdf"><code>on-off-coverage.pdf</code></a>: Relationship between covered on-target bases and covered off-target bases in exome-seq data, with varying extensions of the target region to allow for &quot;near-target&quot; capture.</li>
+</ul>

examples/Salomon/CD4/reports/ChIP-seq/index.html

@@ -0,0 +1,5 @@
+<ul>
+<li><a href="H3K4me2-exploration.html"><code>H3K4me2-exploration.html</code></a>, <a href="H3K4me3-exploration.html"><code>H3K4me3-exploration.html</code></a>, <a href="H3K27me3-exploration.html"><code>H3K27me3-exploration.html</code></a>: Exploration and QC reports on ChIP-seq data from 3 histone marks</li>
+<li><a href="H3K4me2-diffmod.html"><code>H3K4me2-diffmod.html</code></a>, <a href="H3K4me3-diffmod.html"><code>H3K4me3-diffmod.html</code></a>, <a href="H3K27me3-diffmod.html"><code>H3K27me3-diffmod.html</code></a>: Differential modification reports for three histone marks</li>
+<li><a href="peak-sizes.html"><code>peak-sizes.html</code></a>: Analysis of peak sizes for 3 histone marks</li>
+</ul>

examples/Salomon/CD4/reports/RNA-seq/index.html

@@ -0,0 +1,31 @@
+<p>RNA-seq data were analyzed using 5 different quantification strategies and 2 different transcriptome annotations, for 10 total analyses.</p>
+<h2 id="data-exploration-and-qc-reports">Data exploration and QC reports</h2>
+<ul>
+<li><a href="hisat2_grch38_snp_tran_ensembl.85-exploration.html"><code>hisat2_grch38_snp_tran_ensembl.85-exploration.html</code></a></li>
+<li><a href="hisat2_grch38_snp_tran_knownGene-exploration.html"><code>hisat2_grch38_snp_tran_knownGene-exploration.html</code></a></li>
+<li><a href="kallisto_hg38.analysisSet_ensembl.85-exploration.html"><code>kallisto_hg38.analysisSet_ensembl.85-exploration.html</code></a></li>
+<li><a href="kallisto_hg38.analysisSet_knownGene-exploration.html"><code>kallisto_hg38.analysisSet_knownGene-exploration.html</code></a></li>
+<li><a href="salmon_hg38.analysisSet_ensembl.85-exploration.html"><code>salmon_hg38.analysisSet_ensembl.85-exploration.html</code></a></li>
+<li><a href="salmon_hg38.analysisSet_knownGene-exploration.html"><code>salmon_hg38.analysisSet_knownGene-exploration.html</code></a></li>
+<li><a href="shoal_hg38.analysisSet_ensembl.85-exploration.html"><code>shoal_hg38.analysisSet_ensembl.85-exploration.html</code></a></li>
+<li><a href="shoal_hg38.analysisSet_knownGene-exploration.html"><code>shoal_hg38.analysisSet_knownGene-exploration.html</code></a></li>
+<li><a href="star_hg38.analysisSet_ensembl.85-exploration.html"><code>star_hg38.analysisSet_ensembl.85-exploration.html</code></a></li>
+<li><a href="star_hg38.analysisSet_knownGene-exploration.html"><code>star_hg38.analysisSet_knownGene-exploration.html</code></a></li>
+</ul>
+<h2 id="differential-expression-reports">Differential expression reports</h2>
+<ul>
+<li><a href="hisat2_grch38_snp_tran_ensembl.85-diffexp.html"><code>hisat2_grch38_snp_tran_ensembl.85-diffexp.html</code></a></li>
+<li><a href="hisat2_grch38_snp_tran_knownGene-diffexp.html"><code>hisat2_grch38_snp_tran_knownGene-diffexp.html</code></a></li>
+<li><a href="kallisto_hg38.analysisSet_ensembl.85-diffexp.html"><code>kallisto_hg38.analysisSet_ensembl.85-diffexp.html</code></a></li>
+<li><a href="kallisto_hg38.analysisSet_knownGene-diffexp.html"><code>kallisto_hg38.analysisSet_knownGene-diffexp.html</code></a></li>
+<li><a href="salmon_hg38.analysisSet_ensembl.85-diffexp.html"><code>salmon_hg38.analysisSet_ensembl.85-diffexp.html</code></a></li>
+<li><a href="salmon_hg38.analysisSet_knownGene-diffexp.html"><code>salmon_hg38.analysisSet_knownGene-diffexp.html</code></a></li>
+<li><a href="shoal_hg38.analysisSet_ensembl.85-diffexp.html"><code>shoal_hg38.analysisSet_ensembl.85-diffexp.html</code></a></li>
+<li><a href="shoal_hg38.analysisSet_knownGene-diffexp.html"><code>shoal_hg38.analysisSet_knownGene-diffexp.html</code></a></li>
+<li><a href="star_hg38.analysisSet_ensembl.85-diffexp.html"><code>star_hg38.analysisSet_ensembl.85-diffexp.html</code></a></li>
+<li><a href="star_hg38.analysisSet_knownGene-diffexp.html"><code>star_hg38.analysisSet_knownGene-diffexp.html</code></a></li>
+</ul>
+<h2 id="comparison-between-quantification-strategies">Comparison between quantification strategies</h2>
+<ul>
+<li><a href="rnaseq-compare.html"><code>rnaseq-compare.html</code></a></li>
+</ul>

examples/Salomon/CD4/reports/index.html

@@ -0,0 +1,4 @@
+<ul>
+<li><a href="ChIP-seq"><code>ChIP-seq</code></a>: Example reports for ChIP-seq data</li>
+<li><a href="RNA-seq"><code>RNA-seq</code></a>: Example reports for RNA-seq data</li>
+</ul>

examples/Salomon/Pathways/index.html

@@ -0,0 +1,5 @@
+<ul>
+<li><a href="Pathway%20Presentation.pdf"><code>Pathway Presentation.pdf</code></a>: Presentation about differential expression tests for gene sets and pathways</li>
+<li><a href="Cyno%20Pathway%20Summary.pdf"><code>Cyno Pathway Summary.pdf</code></a>: Summary report of significant pathways for an RNA-seq data set</li>
+<li><a href="Pathway%20Analysis%20Example.html"><code>Pathway Analysis Example.html</code></a>: Subset of full output for pathway and gene set tests</li>
+</ul>

examples/Salomon/Teaching/index.html

@@ -0,0 +1,4 @@
+<ul>
+<li><a href="RNA-Seq%20Lecture.pdf"><code>RNA-Seq Lecture.pdf</code></a>: Lecture slides for basic RNA-seq analysis</li>
+<li><a href="RNA-Seq%20Lab.html"><code>RNA-Seq Lab.html</code></a>: Interactive lab for basic RNA-seq analysis</li>
+</ul>

examples/Salomon/fRMA/fRMA_consistency_results/index.html

@@ -0,0 +1,7 @@
+<p>These are a series of plots to assess the effectiveness and consistency of the frozen RMA (fRMA) implementation for blood (PAX) and biopsy (BX) samples, by looking at the relative fold changes of the same data normalized by RNA and five replicate fRMA vector sets.</p>
+<ul>
+<li><a href="M%20Boxplots%20for%20BX.pdf"><code>M Boxplots for BX.pdf</code></a></li>
+<li><a href="M%20Boxplots%20for%20PAX.pdf"><code>M Boxplots for PAX.pdf</code></a></li>
+<li><a href="MA%20Plots%20for%20BX.pdf"><code>MA Plots for BX.pdf</code></a></li>
+<li><a href="MA%20Plots%20for%20PAX.pdf"><code>MA Plots for PAX.pdf</code></a></li>
+</ul>

examples/Salomon/index.html

@@ -0,0 +1,21 @@
+<h2 id="sub-folders">Sub-folders</h2>
+<ul>
+<li><a href="Teaching"><code>Teaching</code></a>: Teaching materials for my lecture and lab on introductory RNA-seq analysis</li>
+<li><a href="CD4"><code>CD4</code></a>: Examples relating to my CD4 memory RNA-seq &amp; ChIP-seq project</li>
+<li><a href="450k"><code>450k</code></a>: Examples relating to analysis of Illumina 450k DNA methylation arrays</li>
+<li><a href="Pathways"><code>Pathways</code></a>: Examples of gene set and pathway analysis for RNA-seq data</li>
+<li><a href="globin"><code>globin</code></a>: Examples of my work in demonstrating the performance of a new globin blocking protocol for RNA-seq of blood tissues</li>
+<li><a href="fRMA"><code>fRMA</code></a>: Examples and code from my work creating a custom frozen RMA reference to provide a stable normalization for machine learning applications</li>
+</ul>
+<h2 id="presentations">Presentations</h2>
+<ul>
+<li><a href="DGE%20Presentation.pdf"><code>DGE Presentation.pdf</code></a>: A presentation comparing edgeR, DESeq, and limma on both a conceptual and practical level</li>
+<li><a href="Advanced%20RNA-seq%20Analysis.pdf"><code>Advanced RNA-seq Analysis.pdf</code></a>: A presentation on the advanced features of limma for RNA-seq analysis</li>
+<li><a href="Reproducible%20Workflow%20Presentation.pdf"><code>Reproducible Workflow Presentation.pdf</code></a>:</li>
+</ul>
+<h2 id="other-files">Other files</h2>
+<ul>
+<li><a href="Classifier%20Math%20Write-up.pdf"><code>Classifier Math Write-up.pdf</code></a>: A short write-up to explain the mathematical principles behind the classifier method used in a machine learning project</li>
+<li><a href="blockbuster-pipeline.R.html"><code>blockbuster-pipeline.R.html</code></a>: R code for clustering small RNA reads into clusters using <a href="http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html">Blockbuster</a></li>
+<li><a href="mdsplots-multidim.pdf"><code>mdsplots-multidim.pdf</code></a>: A PCA plot of RNA-seq data for <em>C. elegans</em> samples with and without a drug that retards the aging process, demonstrating smaller age-related changes with the drug (for <a href="https://elifesciences.org/content/4/e08833">this paper</a>)</li>
+</ul>

examples/UVa/index.html

@@ -0,0 +1,6 @@
+<ul>
+<li><a href="contigfarmer.pdf"><code>contigfarmer.pdf</code></a>: My undergraduate thesis describing &quot;Contig Farmer&quot;, a method to extend contigs with overlapping reads when memory is too limited to perform a complete <em>de novo</em> assembly of the whole data set</li>
+<li><a href="blast-slides.pdf"><code>blast-slides.pdf</code></a>: A presentation explaining the basic principles of optimal and heuristic sequence alignment</li>
+<li><a href="probe-selection.R.html"><code>probe-selection.R.html</code></a>: R code to select the 3 most informative probes for each gene in a custom-designed microarray for a non-model organism</li>
+<li><a href="math-history-paper.pdf"><code>math-history-paper.pdf</code></a>: My final paper for History of Methematics class</li>
+</ul>

examples/index.html

@@ -0,0 +1,6 @@
+<ul>
+<li><a href="Salomon"><code>Salomon</code></a>: Examples of my Ph.D. work in Dr. Daniel Salomon's lab at The Scripps Research Insitute</li>
+<li><a href="Gaasterland"><code>Gaasterland</code></a>: Example of my work in <a href="http://igm.ucsd.edu/faculty/profiles/gaasterland.shtml">Terry Gaasterland's</a> lab at UCSD</li>
+<li><a href="UVa"><code>UVa</code></a>: Examples of my work during my undergraduate studies at the University of Virginia</li>
+<li><a href="cufflinks-presentation.pdf"><code>cufflinks-presentation.pdf</code></a>: A slide deck to explain the concepts behind <a href="http://cole-trapnell-lab.github.io/cufflinks/">Cufflinks</a> to the department during my internship at Merck &amp; Co.</li>
+</ul>