fig:quick-pbmc-corrected
fig:tsne-pbmc-uncorrected
fig:tsne-pbmc-rescaled
fig:tsne-pbmc-residuals
fig:tsne-pbmc-corrected
fig:multi-pbmc-corrected
fig:heat-after-mnn
fig:rand-after-mnn
fig:mnn-delta-var-pbmc
fig:pancreas-mnn-delta
fig:pancreas-mnn-delta2
fig:pbmc-marker-blocked
fig:seger-beta-ins-raw
fig:seger-beta-ins-corrected
fig:tsne-initial
fig:heat-cluster-label
fig:md-embryo
fig:mds-embryo
fig:bcvplot
fig:qlplot
fig:allantois-dispersion
fig:exprs-unique-de-allantois
fig:exprs-unique-de-allantois-more
fig:between-label-dge
fig:proxy-ambience
fig:abplotbcv
fig:abplotql
fig:unref-pbmc-filtered-var
fig:unref-filtered-pbmc-variance
fig:unref-filtered-pbmc-tsne
fig:unref-filtered-pbmc-merged-tsne
fig:tsne-pancreas-rescaled
fig:tsne-pancreas-mnn
fig:tsne-pancreas-mnn-many
fig:tsne-pancreas-mnn-donor
fig:tsne-pancreas-mnn-donor-all
fig:unref-umap-merged-hsc
fig:unref-umap-traj-hsc
fig:unref-umap-traj-hsc2
fig:unref-pijuan-var-1
fig:unref-pijuan-var-2
fig:unref-pijuan-var-3
fig:unref-pijuan-tsne
integrating-datasets
motivation
quick-start
slower-setup
no-correction
linear-regression
by-rescaling-the-counts
by-fitting-a-linear-model
mnn-correction
further-options
correction-diagnostics
motivation-1
mixing-between-batches
preserving-biological-heterogeneity
mnn-specific-diagnostics
using-corrected-values
background
for-within-batch-comparisons
after-blocking-on-the-batch
for-between-batch-comparisons
multi-sample-comparisons
motivation-2
setting-up-the-data
creating-pseudo-bulk-samples
performing-the-de-analysis
putting-it-all-together
looping-across-labels
cross-label-meta-analyses
testing-for-between-label-differences
ambient-problems
background-1
filtering-out-affected-degs
by-estimating-ambient-contamination
with-prior-knowledge
without-an-ambient-profile
subtracting-ambient-counts
differential-abundance
overview
performing-the-da-analysis
composition-effects
background-2
assuming-most-labels-do-not-change
removing-the-offending-labels
testing-against-a-log-fold-change-threshold
comments-on-interpretation
de-da-duality
sacrificing-differences
human-pbmcs-10x-genomics
introduction
data-loading
quality-control
normalization
variance-modelling
dimensionality-reduction
clustering
data-integration
merged-pancreas
introduction-1
the-good
the-bad
the-ugly
merged-hsc
introduction-2
data-loading-1
setting-up-the-merge
merging-the-datasets
combined-analyses
chimeric-mouse-embryo-10x-genomics
introduction-3
data-loading-2
quality-control-1
normalization-1
variance-modelling-1
merging
clustering-1
dimensionality-reduction-1