fig:extension-schematic
fig:ccf
fig:ccf-histone
fig:chip-pet-dist
fig:filter-global-dist
fig:filter-local-dist
fig:filter-control-dist
fig:compo-norm-ma
fig:eff-norm-ma
fig:trend-norm-ma
fig:nfya-disp-plot
fig:nfya-disp-rmcheck
fig:nfya-mds-qc
fig:h3k9ac-ccfplot
fig:h3k9ac-bghistplot
fig:h3k9ac-trendplot
fig:h3k9ac-normplot
fig:h3k9ac-bcvplot
fig:h3k9ac-qlplot
fig:h3k9ac-mdsplot
fig:simplebroadplot
fig:complexplot
fig:simplesharpplot
fig:cbp-ccfplot
fig:cbp-compoplot
fig:cbp-bcvplot
fig:cbp-qlplot
fig:cbp-mdsplot
fig:cbp-tfplot
fig:h3k27me3-bghistplot
fig:h3k27me3-compoplot
fig:h3k27me3-bcvplot
fig:h3k27me3-qlplot
fig:h3k27me3-mdsplot
fig:h3k27me3-tfplot
welcome
introduction
how-to-read-this-book
how-to-get-help
how-to-cite-this-book
quick-start
counting-reads-into-windows
background
obtaining-window-level-counts
filtering-out-low-quality-reads
sec:ccf
sec:windowsize
more-counting-options
sec:problematic-regions
sec:efficiency
data:pet
other-counting-strategies
sec:binning
manually-specified-regions
strand-specific-counting
sec:coercelen
chap-filter
overview
by-count-size
by-proportion
sec:global-filter
by-local-enrichment
mimicking-single-sample-peak-callers
identifying-local-maxima-seclocalmax
with-negative-controls
by-prior-information
some-final-comments-about-filtering
chap-norm
overview-1
sec:compo-norm
using-the-tmm-method-on-binned-counts
sec:normbinsize
visualizing-normalization-with-ma-plots
sec:eff-norm
data:norm
filtering-windows-prior-to-normalization
sec:eff-norm-ma
sec:normchoice
with-spike-in-chromatin
dealing-with-trended-biases
a-word-on-other-biases
chap-stats
overview-2
setting-up-for-edger
estimating-the-dispersions
sec:dispest
modelling-variable-dispersions-between-windows
testing-for-db-windows
what-to-do-without-replicates
examining-replicate-similarity-with-mds-plots
correction-for-multiple-testing
overview-3
grouping-windows-into-regions
sec:cluster
using-external-information
obtaining-per-region-p-value
combining-window-level-p-values
sec:mostsig
wrapper-functions
squeezing-out-more-detection-power
sec:bin-integrate
weighting-windows-on-abundance
filtering-after-testing-but-before-correction
fdr-control-in-difficult-situations
clustering-only-on-db-windows-for-diffuse-marks
using-the-empirical-fdr-for-noisy-data
detecting-complex-db
enforcing-a-minimal-number-of-db-windows
annotation-and-visualization
sec:detail-ranges
checking-bimodality-for-tf-studies
saving-the-results-to-file
simple-visualization-of-genomic-coverage
h3k9ac-pro-b-versus-mature-b
overview-4
pre-processing-checks
examining-mapping-statistics
obtaining-the-encode-blacklist
setting-up-extraction-parameters
quantifying-coverage
computing-the-average-fragment-length
counting-reads-into-windows-1
filtering-windows-by-abundance
normalizing-for-trended-biases
statistical-modelling
estimating-the-nb-dispersion
estimating-the-ql-dispersion
examining-the-data-with-mds-plots
testing-for-db
interpreting-the-db-results
adding-gene-centric-annotation
using-the-chippeakanno-package
reporting-gene-based-results
visualizing-db-results
overview-5
simple-db-across-a-broad-region
complex-db-across-a-broad-region
simple-db-across-a-small-region
cbp-wild-type-versus-knock-out
background-1
pre-processing
quantifying-coverage-1
computing-the-average-fragment-length-1
counting-reads-into-windows-2
filtering-of-low-abundance-windows
normalization-for-composition-biases
sec:cbp-statistical-modelling
testing-for-db-1
annotation-and-visualization-1
h3k27me3-wild-type-versus-knock-out
overview-6
pre-processing-checks-1
counting-reads-into-windows-3
filtering-of-low-abundance-windows-1
normalization-for-composition-biases-1
statistical-modelling-1
consolidating-results-from-multiple-window-sizes
annotation-and-visualization-2
contributors
bibliography