Enclose file names in backticks in README files

examples/Salomon/CD4/README.mkdn

@@ -2,28 +2,28 @@ This is a series of example plots and tables from a combined
 RNA-seq/ChIP-seq study on differences between naive and memory T-cell
 activation.
 
-- [p-value distributions.pdf](p-value distributions.pdf) is a series
+- [`p-value distributions.pdf`](p-value distributions.pdf) is a series
   of p-value histograms for each of the contrasts tested. A contrast
   with no significant differential expression would exhibit a uniform
   distribution, while differential expression would be reflected by an
   excess of small p-values.
-- [FPKM by Peak Status H3K4.pdf](FPKM by Peak Status H3K4.pdf) shows
+- [`FPKM by Peak Status H3K4.pdf`](FPKM by Peak Status H3K4.pdf) shows
   the variation in gene expression based on the presence or absence of
   two histone marks in the gene promoters.
-- [promoter-edger-topgenes3-ql.xlsx](promoter-edger-topgenes3-ql.xlsx)
+- [`promoter-edger-topgenes3-ql.xlsx`](promoter-edger-topgenes3-ql.xlsx)
   is a spreadsheet of all promoters with differential histone
   modification in their promoters based on the ChIP-seq read counts.
-- [Promoter Peak Distance Profile.pdf](Promoter Peak Distance Profile.pdf)
+- [`Promoter Peak Distance Profile.pdf`](Promoter Peak Distance Profile.pdf)
   shows the distribution of distances from transcription
   start sites to the nearest peak for the three histone modifications
   studied. This was used to determine the "promoter radius" for read
   counting. Notably, the three histone marks do not all have the same
   promoter radius.
-- [rnaseq-edgeR-vs-limma.pdf](rnaseq-edgeR-vs-limma.pdf) and
-  [rnaseq-limma-weighted-vs-uw.pdf](rnaseq-limma-weighted-vs-uw.pdf)
+- [`rnaseq-edgeR-vs-limma.pdf`](rnaseq-edgeR-vs-limma.pdf) and
+  [`rnaseq-limma-weighted-vs-uw.pdf`](rnaseq-limma-weighted-vs-uw.pdf)
   show comparisons of p-values for all genes in each contrast of the
   RNA-seq data, comparing edgeR and limma-voom with/without sample
   quality weights. The final choice of method was limma-voom with
   sample quality weights.
-- [rnaseq-maplots-limma-sampleweights.pdf](rnaseq-maplots-limma-sampleweights.pdf)
+- [`rnaseq-maplots-limma-sampleweights.pdf`](rnaseq-maplots-limma-sampleweights.pdf)
   shows the MA plot for each contrast of the RNA-seq data

examples/Salomon/globin/README.mkdn

@@ -3,11 +3,11 @@
 This is a pair of spreadsheets summarizing the globin-reducing
 properties of an experimental RNA-seq protocol.
 
-- [method-select.xlsx](method-select.xlsx) shows the results for
+- [`method-select.xlsx`](method-select.xlsx) shows the results for
   several different methods of globin reduction. The most important
   column is "Non-HB", which represents the fraction of total reads
   that map to non-globin genes.
-- [concentration-select.xlsx](concentration-select.xlsx) shows the
+- [`concentration-select.xlsx`](concentration-select.xlsx) shows the
   results of selecting the best globin blocking method and optimizing
   the concentration of blockers as well as the number of
   hybridizations.
@@ -17,17 +17,17 @@ properties of an experimental RNA-seq protocol.
 This is a series of example plots for evaluation of a similar globin
 reduction protocol that was designed for cynomolgus monkeys.
 
-- [BCVplots.pdf](BCVplots.pdf) and [corrplot.pdf](corrplot.pdf) show,
-  respectively, that the biological coefficient of variation is not
-  increased, and the sample-to-sample correlation is not decreased, by
-  the globin reduction protocol.
-- [cyno-vs-hg19.pdf](cyno-vs-hg19.pdf) shows excellent correlation
+- [`BCVplots.pdf`](BCVplots.pdf) and [`corrplot.pdf`](corrplot.pdf)
+  show, respectively, that the biological coefficient of variation is
+  not increased, and the sample-to-sample correlation is not
+  decreased, by the globin reduction protocol.
+- [`cyno-vs-hg19.pdf`](cyno-vs-hg19.pdf) shows excellent correlation
   between total read counts on the cyno and human genomes, indicating
   that the cyno annotation is reasonably complete.
-- [maplot.pdf](maplot.pdf) shows an MA plot of the effects of globin
+- [`maplot.pdf`](maplot.pdf) shows an MA plot of the effects of globin
   reduction. Notably, there are real and significant effects on
   non-globin genes, but they are consistent and predictable.
-- [pval-comparisons.pdf](pval-comparisons.pdf) shows the comparison
+- [`pval-comparisons.pdf`](pval-comparisons.pdf) shows the comparison
   between p-values from edgeR, limma-voom, and DESeq2 on the exact
   same differential expression test. Surprisingly, despite the
   significant algorithmic differences, edgeR and limma are in quite