id,file,text
annotation-and-visualization,annotation-and-visualization.html,8
sec:detail-ranges,annotation-and-visualization.html,8.1
checking-bimodality-for-tf-studies,annotation-and-visualization.html,8.2
saving-the-results-to-file,annotation-and-visualization.html,8.3
simple-visualization-of-genomic-coverage,annotation-and-visualization.html,8.4
bibliography,bibliography.html,13
cbp-wild-type-versus-knock-out,cbp-wild-type-versus-knock-out.html,10
background-1,cbp-wild-type-versus-knock-out.html,10.1
pre-processing,cbp-wild-type-versus-knock-out.html,10.2
quantifying-coverage-1,cbp-wild-type-versus-knock-out.html,10.3
computing-the-average-fragment-length-1,cbp-wild-type-versus-knock-out.html,10.3.1
counting-reads-into-windows-2,cbp-wild-type-versus-knock-out.html,10.3.2
filtering-of-low-abundance-windows,cbp-wild-type-versus-knock-out.html,10.4
normalization-for-composition-biases,cbp-wild-type-versus-knock-out.html,10.5
sec:cbp-statistical-modelling,cbp-wild-type-versus-knock-out.html,10.6
testing-for-db-1,cbp-wild-type-versus-knock-out.html,10.7
annotation-and-visualization-1,cbp-wild-type-versus-knock-out.html,10.8
fig:cbp-ccfplot,cbp-wild-type-versus-knock-out.html,10.1
fig:cbp-compoplot,cbp-wild-type-versus-knock-out.html,10.2
fig:cbp-bcvplot,cbp-wild-type-versus-knock-out.html,10.3
fig:cbp-qlplot,cbp-wild-type-versus-knock-out.html,10.4
fig:cbp-mdsplot,cbp-wild-type-versus-knock-out.html,10.5
fig:cbp-tfplot,cbp-wild-type-versus-knock-out.html,10.6
chap-filter,chap-filter.html,4
overview,chap-filter.html,4.1
by-count-size,chap-filter.html,4.2
by-proportion,chap-filter.html,4.3
sec:global-filter,chap-filter.html,4.4
by-local-enrichment,chap-filter.html,4.5
mimicking-single-sample-peak-callers,chap-filter.html,4.5.1
identifying-local-maxima-seclocalmax,chap-filter.html,4.5.2
with-negative-controls,chap-filter.html,4.6
by-prior-information,chap-filter.html,4.7
some-final-comments-about-filtering,chap-filter.html,4.8
fig:filter-global-dist,chap-filter.html,4.1
fig:filter-local-dist,chap-filter.html,4.2
fig:filter-control-dist,chap-filter.html,4.3
chap-norm,chap-norm.html,5
overview-1,chap-norm.html,5.1
sec:compo-norm,chap-norm.html,5.2
using-the-tmm-method-on-binned-counts,chap-norm.html,5.2.1
sec:normbinsize,chap-norm.html,5.2.2
visualizing-normalization-with-ma-plots,chap-norm.html,5.2.3
sec:eff-norm,chap-norm.html,5.3
data:norm,chap-norm.html,5.3.0.1
filtering-windows-prior-to-normalization,chap-norm.html,5.3.1
sec:eff-norm-ma,chap-norm.html,5.3.2
sec:normchoice,chap-norm.html,5.4
with-spike-in-chromatin,chap-norm.html,5.5
dealing-with-trended-biases,chap-norm.html,5.6
a-word-on-other-biases,chap-norm.html,5.7
fig:compo-norm-ma,chap-norm.html,5.1
fig:eff-norm-ma,chap-norm.html,5.2
fig:trend-norm-ma,chap-norm.html,5.3
chap-stats,chap-stats.html,6
overview-2,chap-stats.html,6.1
setting-up-for-placeholder,chap-stats.html,6.2
estimating-the-dispersions,chap-stats.html,6.3
sec:dispest,chap-stats.html,6.3.1
modelling-variable-dispersions-between-windows,chap-stats.html,6.3.2
testing-for-db-windows,chap-stats.html,6.4
what-to-do-without-replicates,chap-stats.html,6.5
examining-replicate-similarity-with-mds-plots,chap-stats.html,6.6
fig:nfya-disp-plot,chap-stats.html,6.1
fig:nfya-disp-rmcheck,chap-stats.html,6.2
fig:nfya-mds-qc,chap-stats.html,6.3
contributors,contributors.html,12
correction-for-multiple-testing,correction-for-multiple-testing.html,7
overview-3,correction-for-multiple-testing.html,7.1
grouping-windows-into-regions,correction-for-multiple-testing.html,7.2
sec:cluster,correction-for-multiple-testing.html,7.2.1
using-external-information,correction-for-multiple-testing.html,7.2.2
obtaining-per-region-p-value,correction-for-multiple-testing.html,7.3
combining-window-level-p-values,correction-for-multiple-testing.html,7.3.1
sec:mostsig,correction-for-multiple-testing.html,7.3.2
wrapper-functions,correction-for-multiple-testing.html,7.3.3
squeezing-out-more-detection-power,correction-for-multiple-testing.html,7.4
sec:bin-integrate,correction-for-multiple-testing.html,7.4.1
weighting-windows-on-abundance,correction-for-multiple-testing.html,7.4.2
filtering-after-testing-but-before-correction,correction-for-multiple-testing.html,7.4.3
fdr-control-in-difficult-situations,correction-for-multiple-testing.html,7.5
clustering-only-on-db-windows-for-diffuse-marks,correction-for-multiple-testing.html,7.5.1
using-the-empirical-fdr-for-noisy-data,correction-for-multiple-testing.html,7.5.2
detecting-complex-db,correction-for-multiple-testing.html,7.5.3
enforcing-a-minimal-number-of-db-windows,correction-for-multiple-testing.html,7.5.4
counting-reads-into-windows,counting-reads-into-windows.html,2
background,counting-reads-into-windows.html,2.1
obtaining-window-level-counts,counting-reads-into-windows.html,2.2
filtering-out-low-quality-reads,counting-reads-into-windows.html,2.3
sec:ccf,counting-reads-into-windows.html,2.4
sec:windowsize,counting-reads-into-windows.html,2.5
fig:extension-schematic,counting-reads-into-windows.html,2.1
fig:ccf,counting-reads-into-windows.html,2.2
fig:ccf-histone,counting-reads-into-windows.html,2.3
h3k27me3-wild-type-versus-knock-out,h3k27me3-wild-type-versus-knock-out.html,11
overview-6,h3k27me3-wild-type-versus-knock-out.html,11.1
pre-processing-checks-1,h3k27me3-wild-type-versus-knock-out.html,11.2
counting-reads-into-windows-3,h3k27me3-wild-type-versus-knock-out.html,11.3
filtering-of-low-abundance-windows-1,h3k27me3-wild-type-versus-knock-out.html,11.4
normalization-for-composition-biases-1,h3k27me3-wild-type-versus-knock-out.html,11.5
statistical-modelling-1,h3k27me3-wild-type-versus-knock-out.html,11.6
consolidating-results-from-multiple-window-sizes,h3k27me3-wild-type-versus-knock-out.html,11.7
annotation-and-visualization-2,h3k27me3-wild-type-versus-knock-out.html,11.8
fig:h3k27me3-bghistplot,h3k27me3-wild-type-versus-knock-out.html,11.1
fig:h3k27me3-compoplot,h3k27me3-wild-type-versus-knock-out.html,11.2
fig:h3k27me3-bcvplot,h3k27me3-wild-type-versus-knock-out.html,11.3
fig:h3k27me3-qlplot,h3k27me3-wild-type-versus-knock-out.html,11.4
fig:h3k27me3-mdsplot,h3k27me3-wild-type-versus-knock-out.html,11.5
fig:h3k27me3-tfplot,h3k27me3-wild-type-versus-knock-out.html,11.6
h3k9ac-pro-b-versus-mature-b,h3k9ac-pro-b-versus-mature-b.html,9
overview-4,h3k9ac-pro-b-versus-mature-b.html,9.1
pre-processing-checks,h3k9ac-pro-b-versus-mature-b.html,9.2
examining-mapping-statistics,h3k9ac-pro-b-versus-mature-b.html,9.2.1
obtaining-the-encode-blacklist,h3k9ac-pro-b-versus-mature-b.html,9.2.2
setting-up-extraction-parameters,h3k9ac-pro-b-versus-mature-b.html,9.2.3
quantifying-coverage,h3k9ac-pro-b-versus-mature-b.html,9.3
computing-the-average-fragment-length,h3k9ac-pro-b-versus-mature-b.html,9.3.1
counting-reads-into-windows-1,h3k9ac-pro-b-versus-mature-b.html,9.3.2
filtering-windows-by-abundance,h3k9ac-pro-b-versus-mature-b.html,9.4
normalizing-for-trended-biases,h3k9ac-pro-b-versus-mature-b.html,9.5
statistical-modelling,h3k9ac-pro-b-versus-mature-b.html,9.6
estimating-the-nb-dispersion,h3k9ac-pro-b-versus-mature-b.html,9.6.1
estimating-the-ql-dispersion,h3k9ac-pro-b-versus-mature-b.html,9.6.2
examining-the-data-with-mds-plots,h3k9ac-pro-b-versus-mature-b.html,9.6.3
testing-for-db,h3k9ac-pro-b-versus-mature-b.html,9.7
interpreting-the-db-results,h3k9ac-pro-b-versus-mature-b.html,9.8
adding-gene-centric-annotation,h3k9ac-pro-b-versus-mature-b.html,9.8.1
using-the-placeholder-package,h3k9ac-pro-b-versus-mature-b.html,9.8.2
reporting-gene-based-results,h3k9ac-pro-b-versus-mature-b.html,9.8.3
visualizing-db-results,h3k9ac-pro-b-versus-mature-b.html,9.9
overview-5,h3k9ac-pro-b-versus-mature-b.html,9.9.1
simple-db-across-a-broad-region,h3k9ac-pro-b-versus-mature-b.html,9.9.2
complex-db-across-a-broad-region,h3k9ac-pro-b-versus-mature-b.html,9.10
simple-db-across-a-small-region,h3k9ac-pro-b-versus-mature-b.html,9.10.1
fig:h3k9ac-ccfplot,h3k9ac-pro-b-versus-mature-b.html,9.1
fig:h3k9ac-bghistplot,h3k9ac-pro-b-versus-mature-b.html,9.2
fig:h3k9ac-trendplot,h3k9ac-pro-b-versus-mature-b.html,9.3
fig:h3k9ac-normplot,h3k9ac-pro-b-versus-mature-b.html,9.4
fig:h3k9ac-bcvplot,h3k9ac-pro-b-versus-mature-b.html,9.5
fig:h3k9ac-qlplot,h3k9ac-pro-b-versus-mature-b.html,9.6
fig:h3k9ac-mdsplot,h3k9ac-pro-b-versus-mature-b.html,9.7
fig:simplebroadplot,h3k9ac-pro-b-versus-mature-b.html,9.8
fig:complexplot,h3k9ac-pro-b-versus-mature-b.html,9.9
fig:simplesharpplot,h3k9ac-pro-b-versus-mature-b.html,9.10
welcome,index.html,1
introduction,index.html,1.1
how-to-read-this-book,index.html,1.2
how-to-get-help,index.html,1.3
how-to-cite-this-book,index.html,1.4
quick-start,index.html,1.5
more-counting-options,more-counting-options.html,3
sec:problematic-regions,more-counting-options.html,3.1
sec:efficiency,more-counting-options.html,3.2
data:pet,more-counting-options.html,3.3
other-counting-strategies,more-counting-options.html,3.4
sec:binning,more-counting-options.html,3.4.1
manually-specified-regions,more-counting-options.html,3.4.2
strand-specific-counting,more-counting-options.html,3.4.3
sec:coercelen,more-counting-options.html,3.5
fig:chip-pet-dist,more-counting-options.html,3.1
