Mark a bunch of TODOs done

thesis.lyx

@@ -388,28 +388,6 @@ Check all figures to make sure they fit on the page with their legends.
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-Look into auto-generated nomenclature list: 
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- Otherwise, do a manual pass for all abbreviations at the end.
- Do nomenclature/abbreviations independently for each chapter.
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@@ -620,21 +598,6 @@ Rethink the subsection organization after the intro is written.
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-Citations are needed all over the place.
- A lot of this is knowledge I've just absorbed from years of conversation
- in the Salomon lab, without ever having seen a citation for it.
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@@ -6536,22 +6499,6 @@ literal "false"
  for H3K27me3.
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-I also have some figures looking at interactions between marks (e.g.
- what if a promoter has both H3K4me3 and H3K27me3), but I don't know if
- that much detail is warranted here, since all the effects just seem approximate
-ly additive anyway.
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 Gene expression and promoter histone methylation patterns in naïve and memory
  show convergence at day 14
@@ -7266,19 +7213,6 @@ PCoA plots for promoter ChIP-seq and expression RNA-seq data
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-Check up on figure refs in this paragraph
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-RNA-seq values in the plots use logCPM but should really use logFPKM or
- logTPM.
- Fix if time allows.
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 Should have a table of p-values on difference of means between Cluster 5
  and the others.
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-Is there more to say here?
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-Should maybe re-explain what was done or refer back to the previous section.
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@@ -9128,27 +9021,6 @@ kb radius determined from TSS-to-peak distances is functionally significant.
  levels both have interesting features within this radius.
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-My instinct is to say 
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-further study is needed
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- here, but that goes in Chapter 5, right?
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 Convergence
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