Add a README.mkdn for every directory

examples/Gaasterland/README.mkdn

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+- [`delox.R.html`](delox.R.html): The R code
+  for
+  [Deloxer](https://academic.oup.com/nar/article/40/3/e24/1128321/Illumina-mate-paired-DNA-sequencing-library)
+- [`depth-consistency.pdf`](depth-consistency.pdf): Visualization of
+  consistency of coverage depth between 2 Exome sequencing replicates
+- [`illumina-qc.html`](illumina-qc.html): QC chart indicating quality
+  score dropoff along read length for exome sequencing data set.
+- [`ipi-results-small.txt`](ipi-results-small.txt): A sample of output
+  showing alignment of *de novo* 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.
+- [`mirna-results.html`](mirna-results.html): Example output from
+  miRNA binding site predictions
+- [`neartarget.pdf`](neartarget.pdf): Visualization of mean coverage
+  depth in exome sequencing data in the regions flanking the probe
+  targets.
+- [`on-off-coverage.pdf`](on-off-coverage.pdf): 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
+  "near-target" capture.

examples/README.mkdn

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+- [`Salomon`](Salomon): Examples of my Ph.D. work in Dr. Daniel
+  Salomon's lab at The Scripps Research Insitute
+- [`Gaasterland`](Gaasterland): Example of my work in
+  [Terry Gaasterland's](http://igm.ucsd.edu/faculty/profiles/gaasterland.shtml) 
+  lab at UCSD
+- [`UVa`](UVa): Examples of my work during my undergraduate studies at
+  the University of Virginia
+- [`cufflinks-presentation.pdf`](cufflinks-presentation.pdf): A slide
+  deck to explain the concepts
+  behind [Cufflinks](http://cole-trapnell-lab.github.io/cufflinks/) to
+  the department during my internship at Merck & Co.

examples/Salomon/CD4/reports/ChIP-seq/README.mkdn

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+- [`H3K4me2-exploration.html`](H3K4me2-exploration.html),
+  [`H3K4me3-exploration.html`](H3K4me3-exploration.html),
+  [`H3K27me3-exploration.html`](H3K27me3-exploration.html):
+  Exploration and QC reports on ChIP-seq data from 3 histone marks
+- [`H3K4me2-diffmod.html`](H3K4me2-diffmod.html),
+  [`H3K4me3-diffmod.html`](H3K4me3-diffmod.html),
+  [`H3K27me3-diffmod.html`](H3K27me3-diffmod.html): Differential
+  modification reports for three histone marks
+- [`peak-sizes.html`](peak-sizes.html): Analysis of peak sizes for 3
+  histone marks

examples/Salomon/CD4/reports/README.mkdn

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+- [`ChIP-seq`](ChIP-seq): Example reports for ChIP-seq data
+- [`RNA-seq`](RNA-seq): Example reports for RNA-seq data

examples/Salomon/CD4/reports/RNA-seq/README.mkdn

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+RNA-seq data were analyzed using 5 different quantification strategies
+and 2 different transcriptome annotations, for 10 total analyses.
+
+## Data exploration and QC reports
+
+- [`hisat2_grch38_snp_tran_ensembl.85-exploration.html`](hisat2_grch38_snp_tran_ensembl.85-exploration.html)
+- [`hisat2_grch38_snp_tran_knownGene-exploration.html`](hisat2_grch38_snp_tran_knownGene-exploration.html)
+- [`kallisto_hg38.analysisSet_ensembl.85-exploration.html`](kallisto_hg38.analysisSet_ensembl.85-exploration.html)
+- [`kallisto_hg38.analysisSet_knownGene-exploration.html`](kallisto_hg38.analysisSet_knownGene-exploration.html)
+- [`salmon_hg38.analysisSet_ensembl.85-exploration.html`](salmon_hg38.analysisSet_ensembl.85-exploration.html)
+- [`salmon_hg38.analysisSet_knownGene-exploration.html`](salmon_hg38.analysisSet_knownGene-exploration.html)
+- [`shoal_hg38.analysisSet_ensembl.85-exploration.html`](shoal_hg38.analysisSet_ensembl.85-exploration.html)
+- [`shoal_hg38.analysisSet_knownGene-exploration.html`](shoal_hg38.analysisSet_knownGene-exploration.html)
+- [`star_hg38.analysisSet_ensembl.85-exploration.html`](star_hg38.analysisSet_ensembl.85-exploration.html)
+- [`star_hg38.analysisSet_knownGene-exploration.html`](star_hg38.analysisSet_knownGene-exploration.html)
+
+## Differential expression reports
+
+- [`hisat2_grch38_snp_tran_ensembl.85-diffexp.html`](hisat2_grch38_snp_tran_ensembl.85-diffexp.html)
+- [`hisat2_grch38_snp_tran_knownGene-diffexp.html`](hisat2_grch38_snp_tran_knownGene-diffexp.html)
+- [`kallisto_hg38.analysisSet_ensembl.85-diffexp.html`](kallisto_hg38.analysisSet_ensembl.85-diffexp.html)
+- [`kallisto_hg38.analysisSet_knownGene-diffexp.html`](kallisto_hg38.analysisSet_knownGene-diffexp.html)
+- [`salmon_hg38.analysisSet_ensembl.85-diffexp.html`](salmon_hg38.analysisSet_ensembl.85-diffexp.html)
+- [`salmon_hg38.analysisSet_knownGene-diffexp.html`](salmon_hg38.analysisSet_knownGene-diffexp.html)
+- [`shoal_hg38.analysisSet_ensembl.85-diffexp.html`](shoal_hg38.analysisSet_ensembl.85-diffexp.html)
+- [`shoal_hg38.analysisSet_knownGene-diffexp.html`](shoal_hg38.analysisSet_knownGene-diffexp.html)
+- [`star_hg38.analysisSet_ensembl.85-diffexp.html`](star_hg38.analysisSet_ensembl.85-diffexp.html)
+- [`star_hg38.analysisSet_knownGene-diffexp.html`](star_hg38.analysisSet_knownGene-diffexp.html)
+
+## Comparison between quantification strategies
+
+- [`rnaseq-compare.html`](rnaseq-compare.html)

examples/Salomon/Pathways/README.mkdn

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+- [`Pathway Presentation.pdf`](Pathway Presentation.pdf): Presentation
+  about differential expression tests for gene sets and pathways
+- [`Cyno Pathway Summary.pdf`](Cyno Pathway Summary.pdf): Summary
+  report of significant pathways for an RNA-seq data set
+- [`Pathway Analysis Example.html`](Pathway Analysis Example.html):
+  Subset of full output for pathway and gene set tests

examples/Salomon/README.mkdn

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

examples/Salomon/Teaching/README.mkdn

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+- [`RNA-Seq Lecture.pdf`](RNA-Seq Lecture.pdf): Lecture slides for basic RNA-seq analysis
+- [`RNA-Seq Lab.html`](RNA-Seq Lab.html): Interactive lab for basic RNA-seq analysis

examples/Salomon/fRMA/fRMA_consistency_results/README.mkdn

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+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.
+
+- [`M Boxplots for BX.pdf`](M Boxplots for BX.pdf)
+- [`M Boxplots for PAX.pdf`](M Boxplots for PAX.pdf)
+- [`MA Plots for BX.pdf`](MA Plots for BX.pdf)
+- [`MA Plots for PAX.pdf`](MA Plots for PAX.pdf)

examples/UVa/README.mkdn

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+- [`contigfarmer.pdf`](contigfarmer.pdf): My undergraduate thesis
+  describing "Contig Farmer", a method to extend contigs with
+  overlapping reads when memory is too limited to perform a complete
+  *de novo* assembly of the whole data set
+- [`blast-slides.pdf`](blast-slides.pdf): A presentation explaining
+  the basic principles of optimal and heuristic sequence alignment
+- [`probe-selection.R.html`](probe-selection.R.html): R code to select
+  the 3 most informative probes for each gene in a custom-designed
+  microarray for a non-model organism
+- [`math-history-paper.pdf`](math-history-paper.pdf): My final paper
+  for History of Methematics class