id,file,text
ambient-problems,ambient-problems.html,5
background-1,ambient-problems.html,5.1
filtering-out-affected-degs,ambient-problems.html,5.2
by-estimating-ambient-contamination,ambient-problems.html,5.2.1
with-prior-knowledge,ambient-problems.html,5.2.2
without-an-ambient-profile,ambient-problems.html,5.2.3
subtracting-ambient-counts,ambient-problems.html,5.3
fig:proxy-ambience,ambient-problems.html,5.1
chimeric-mouse-embryo-10x-genomics,chimeric-mouse-embryo-10x-genomics.html,10
introduction-3,chimeric-mouse-embryo-10x-genomics.html,10.1
data-loading-2,chimeric-mouse-embryo-10x-genomics.html,10.2
quality-control-1,chimeric-mouse-embryo-10x-genomics.html,10.3
normalization-1,chimeric-mouse-embryo-10x-genomics.html,10.4
variance-modelling-1,chimeric-mouse-embryo-10x-genomics.html,10.5
merging,chimeric-mouse-embryo-10x-genomics.html,10.6
clustering-1,chimeric-mouse-embryo-10x-genomics.html,10.7
dimensionality-reduction-1,chimeric-mouse-embryo-10x-genomics.html,10.8
fig:unref-pijuan-var,chimeric-mouse-embryo-10x-genomics.html,10.1
fig:unref-pijuan-tsne,chimeric-mouse-embryo-10x-genomics.html,10.2
correction-diagnostics,correction-diagnostics.html,2
motivation-1,correction-diagnostics.html,2.1
mixing-between-batches,correction-diagnostics.html,2.2
preserving-biological-heterogeneity,correction-diagnostics.html,2.3
mnn-specific-diagnostics,correction-diagnostics.html,2.4
fig:heat-after-mnn,correction-diagnostics.html,2.1
fig:rand-after-mnn,correction-diagnostics.html,2.2
fig:mnn-delta-var-pbmc,correction-diagnostics.html,2.3
differential-abundance,differential-abundance.html,6
overview,differential-abundance.html,6.1
performing-the-da-analysis,differential-abundance.html,6.2
composition-effects,differential-abundance.html,6.3
background-2,differential-abundance.html,6.3.1
assuming-most-labels-do-not-change,differential-abundance.html,6.3.2
removing-the-offending-labels,differential-abundance.html,6.3.3
testing-against-a-log-fold-change-threshold,differential-abundance.html,6.3.4
comments-on-interpretation,differential-abundance.html,6.4
de-da-duality,differential-abundance.html,6.4.1
sacrificing-differences,differential-abundance.html,6.4.2
fig:abplotbcv,differential-abundance.html,6.1
fig:abplotql,differential-abundance.html,6.2
human-pbmcs-10x-genomics,human-pbmcs-10x-genomics.html,7
introduction,human-pbmcs-10x-genomics.html,7.1
data-loading,human-pbmcs-10x-genomics.html,7.2
quality-control,human-pbmcs-10x-genomics.html,7.3
normalization,human-pbmcs-10x-genomics.html,7.4
variance-modelling,human-pbmcs-10x-genomics.html,7.5
dimensionality-reduction,human-pbmcs-10x-genomics.html,7.6
clustering,human-pbmcs-10x-genomics.html,7.7
data-integration,human-pbmcs-10x-genomics.html,7.8
fig:unref-pbmc-filtered-var,human-pbmcs-10x-genomics.html,7.1
fig:unref-filtered-pbmc-variance,human-pbmcs-10x-genomics.html,7.2
fig:unref-filtered-pbmc-tsne,human-pbmcs-10x-genomics.html,7.3
fig:unref-filtered-pbmc-merged-tsne,human-pbmcs-10x-genomics.html,7.4
integrating-datasets,integrating-datasets.html,1
motivation,integrating-datasets.html,1.1
quick-start,integrating-datasets.html,1.2
slower-setup,integrating-datasets.html,1.3
no-correction,integrating-datasets.html,1.4
linear-regression,integrating-datasets.html,1.5
by-rescaling-the-counts,integrating-datasets.html,1.5.1
by-fitting-a-linear-model,integrating-datasets.html,1.5.2
mnn-correction,integrating-datasets.html,1.6
further-options,integrating-datasets.html,1.7
fig:quick-pbmc-corrected,integrating-datasets.html,1.1
fig:tsne-pbmc-uncorrected,integrating-datasets.html,1.2
fig:tsne-pbmc-rescaled,integrating-datasets.html,1.3
fig:tsne-pbmc-residuals,integrating-datasets.html,1.4
fig:tsne-pbmc-corrected,integrating-datasets.html,1.5
fig:multi-pbmc-corrected,integrating-datasets.html,1.6
merged-hsc,merged-hsc.html,9
introduction-2,merged-hsc.html,9.1
data-loading-1,merged-hsc.html,9.2
setting-up-the-merge,merged-hsc.html,9.3
merging-the-datasets,merged-hsc.html,9.4
combined-analyses,merged-hsc.html,9.5
fig:unref-umap-merged-hsc,merged-hsc.html,9.1
fig:unref-umap-traj-hsc,merged-hsc.html,9.2
fig:unref-umap-traj-hsc2,merged-hsc.html,9.3
merged-pancreas,merged-pancreas.html,8
introduction-1,merged-pancreas.html,8.1
the-good,merged-pancreas.html,8.2
the-bad,merged-pancreas.html,8.3
the-ugly,merged-pancreas.html,8.4
fig:tsne-pancreas-rescaled,merged-pancreas.html,8.1
fig:tsne-pancreas-mnn,merged-pancreas.html,8.2
fig:tsne-pancreas-mnn-many,merged-pancreas.html,8.3
fig:tsne-pancreas-mnn-donor,merged-pancreas.html,8.4
fig:tsne-pancreas-mnn-donor-all,merged-pancreas.html,8.5
multi-sample-comparisons,multi-sample-comparisons.html,4
motivation-2,multi-sample-comparisons.html,4.1
setting-up-the-data,multi-sample-comparisons.html,4.2
creating-pseudo-bulk-samples,multi-sample-comparisons.html,4.3
performing-the-de-analysis,multi-sample-comparisons.html,4.4
putting-it-all-together,multi-sample-comparisons.html,4.5
looping-across-labels,multi-sample-comparisons.html,4.5.1
cross-label-meta-analyses,multi-sample-comparisons.html,4.5.2
testing-for-between-label-differences,multi-sample-comparisons.html,4.6
fig:tsne-initial,multi-sample-comparisons.html,4.1
fig:heat-cluster-label,multi-sample-comparisons.html,4.2
fig:md-embryo,multi-sample-comparisons.html,4.3
fig:mds-embryo,multi-sample-comparisons.html,4.4
fig:bcvplot,multi-sample-comparisons.html,4.5
fig:qlplot,multi-sample-comparisons.html,4.6
fig:allantois-dispersion,multi-sample-comparisons.html,4.7
fig:exprs-unique-de-allantois,multi-sample-comparisons.html,4.8
fig:exprs-unique-de-allantois-more,multi-sample-comparisons.html,4.9
fig:between-label-dge,multi-sample-comparisons.html,4.10
using-corrected-values,using-corrected-values.html,3
background,using-corrected-values.html,3.1
for-within-batch-comparisons,using-corrected-values.html,3.2
after-blocking-on-the-batch,using-corrected-values.html,3.3
for-between-batch-comparisons,using-corrected-values.html,3.4
fig:pancreas-mnn-delta,using-corrected-values.html,3.1
fig:pancreas-mnn-delta2,using-corrected-values.html,3.2
fig:pbmc-marker-blocked,using-corrected-values.html,3.3
fig:seger-beta-ins-raw,using-corrected-values.html,3.4
fig:seger-beta-ins-corrected,using-corrected-values.html,3.5
