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@@ -36,17 +36,21 @@ activation. You can view the (old and messy) code for these plots
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- [`rnaseq-maplots-limma-sampleweights.pdf`](rnaseq-maplots-limma-sampleweights.pdf)
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shows the MA plot for each contrast of the RNA-seq data
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-
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There are also some plots from an in-progress analysis of the same
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data based on sliding windows, rather than just analyzing promoter
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-regions. You can view the code for generating these plots [here][2].
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+regions. You can view the code for generating these plots [here][2],
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+and you can view some presentation slides based on this analysis
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+[here][3].
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[2]: https://github.com/DarwinAwardWinner/CD4-csaw
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+[3]:
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- [`CCF-plots.pdf`](CCF-plots.pdf) shows the cross-correlation
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functions of several different histone marks, at several different
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levels of smoothing. This plot is used to determine the fragment
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- size.
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+ size. You can also observe from the periodic wave-like pattern that
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+ multiple adjacent histones tend to share the same histone
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+ modification.
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- [`site-profile-plots.pdf`](site-profile-plots.pdf) shows plots of
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the relative coverage depth profiles around local coverage maxima.
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This plot is used to determine the footprint size of the protein
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