id,file,text
bach-mouse-mammary-gland-10x-genomics,bach-mouse-mammary-gland-10x-genomics.html,12
introduction-11,bach-mouse-mammary-gland-10x-genomics.html,12.1
data-loading-11,bach-mouse-mammary-gland-10x-genomics.html,12.2
quality-control-11,bach-mouse-mammary-gland-10x-genomics.html,12.3
normalization-11,bach-mouse-mammary-gland-10x-genomics.html,12.4
variance-modelling-10,bach-mouse-mammary-gland-10x-genomics.html,12.5
dimensionality-reduction-11,bach-mouse-mammary-gland-10x-genomics.html,12.6
clustering-11,bach-mouse-mammary-gland-10x-genomics.html,12.7
fig:unref-bach-qc-dist,bach-mouse-mammary-gland-10x-genomics.html,12.1
fig:unref-bach-qc-comp,bach-mouse-mammary-gland-10x-genomics.html,12.2
fig:unref-bach-norm,bach-mouse-mammary-gland-10x-genomics.html,12.3
fig:unref-bach-var,bach-mouse-mammary-gland-10x-genomics.html,12.4
fig:unref-bach-tsne,bach-mouse-mammary-gland-10x-genomics.html,12.5
grun-human-pancreas-cel-seq2,grun-human-pancreas-cel-seq2.html,5
introduction-4,grun-human-pancreas-cel-seq2.html,5.1
data-loading-4,grun-human-pancreas-cel-seq2.html,5.2
quality-control-4,grun-human-pancreas-cel-seq2.html,5.3
normalization-4,grun-human-pancreas-cel-seq2.html,5.4
variance-modelling-3,grun-human-pancreas-cel-seq2.html,5.5
data-integration,grun-human-pancreas-cel-seq2.html,5.6
dimensionality-reduction-4,grun-human-pancreas-cel-seq2.html,5.7
clustering-4,grun-human-pancreas-cel-seq2.html,5.8
fig:unref-grun-qc-dist,grun-human-pancreas-cel-seq2.html,5.1
fig:unref-grun-norm,grun-human-pancreas-cel-seq2.html,5.2
fig:unref-416b-variance,grun-human-pancreas-cel-seq2.html,1.4
fig:unref-grun-tsne,grun-human-pancreas-cel-seq2.html,5.3
grun-mouse-hsc-cel-seq,grun-mouse-hsc-cel-seq.html,9
introduction-8,grun-mouse-hsc-cel-seq.html,9.1
data-loading-8,grun-mouse-hsc-cel-seq.html,9.2
quality-control-8,grun-mouse-hsc-cel-seq.html,9.3
normalization-8,grun-mouse-hsc-cel-seq.html,9.4
variance-modelling-7,grun-mouse-hsc-cel-seq.html,9.5
dimensionality-reduction-8,grun-mouse-hsc-cel-seq.html,9.6
clustering-8,grun-mouse-hsc-cel-seq.html,9.7
marker-gene-detection,grun-mouse-hsc-cel-seq.html,9.8
fig:unref-hgrun-qc-dist,grun-mouse-hsc-cel-seq.html,9.1
fig:unref-hgrun-norm,grun-mouse-hsc-cel-seq.html,9.2
fig:unref-hgrun-var,grun-mouse-hsc-cel-seq.html,9.3
fig:unref-hgrun-tsne,grun-mouse-hsc-cel-seq.html,9.4
fig:unref-heat-hgrun-markers,grun-mouse-hsc-cel-seq.html,9.5
hca-human-bone-marrow-10x-genomics,hca-human-bone-marrow-10x-genomics.html,14
introduction-13,hca-human-bone-marrow-10x-genomics.html,14.1
data-loading-13,hca-human-bone-marrow-10x-genomics.html,14.2
quality-control-13,hca-human-bone-marrow-10x-genomics.html,14.3
normalization-13,hca-human-bone-marrow-10x-genomics.html,14.4
variance-modeling,hca-human-bone-marrow-10x-genomics.html,14.5
data-integration-3,hca-human-bone-marrow-10x-genomics.html,14.6
dimensionality-reduction-13,hca-human-bone-marrow-10x-genomics.html,14.7
clustering-12,hca-human-bone-marrow-10x-genomics.html,14.8
differential-expression,hca-human-bone-marrow-10x-genomics.html,14.9
cell-type-classification,hca-human-bone-marrow-10x-genomics.html,14.10
fig:unref-hca-bone-qc,hca-human-bone-marrow-10x-genomics.html,14.1
fig:unref-hca-bone-mito,hca-human-bone-marrow-10x-genomics.html,14.2
fig:unref-hca-bone-var,hca-human-bone-marrow-10x-genomics.html,14.3
fig:unref-hca-bone-ab,hca-human-bone-marrow-10x-genomics.html,14.4
fig:unref-hca-bone-umap,hca-human-bone-marrow-10x-genomics.html,14.5
fig:unref-hca-bone-dotplot,hca-human-bone-marrow-10x-genomics.html,14.6
human-pbmc-with-surface-proteins-10x-genomics,human-pbmc-with-surface-proteins-10x-genomics.html,4
introduction-3,human-pbmc-with-surface-proteins-10x-genomics.html,4.1
data-loading-3,human-pbmc-with-surface-proteins-10x-genomics.html,4.2
quality-control-3,human-pbmc-with-surface-proteins-10x-genomics.html,4.3
normalization-3,human-pbmc-with-surface-proteins-10x-genomics.html,4.4
dimensionality-reduction-3,human-pbmc-with-surface-proteins-10x-genomics.html,4.5
clustering-3,human-pbmc-with-surface-proteins-10x-genomics.html,4.6
fig:unref-pbmc-adt-qc,human-pbmc-with-surface-proteins-10x-genomics.html,4.1
fig:unref-pbmc-adt-qc-mito,human-pbmc-with-surface-proteins-10x-genomics.html,4.2
fig:unref-norm-pbmc-adt,human-pbmc-with-surface-proteins-10x-genomics.html,4.3
fig:unref-clustmod-pbmc-adt,human-pbmc-with-surface-proteins-10x-genomics.html,4.4
fig:unref-tsne-pbmc-adt,human-pbmc-with-surface-proteins-10x-genomics.html,4.5
lawlor-human-pancreas-smarter,lawlor-human-pancreas-smarter.html,7
introduction-6,lawlor-human-pancreas-smarter.html,7.1
data-loading-6,lawlor-human-pancreas-smarter.html,7.2
quality-control-6,lawlor-human-pancreas-smarter.html,7.3
normalization-6,lawlor-human-pancreas-smarter.html,7.4
variance-modelling-5,lawlor-human-pancreas-smarter.html,7.5
dimensionality-reduction-6,lawlor-human-pancreas-smarter.html,7.6
clustering-6,lawlor-human-pancreas-smarter.html,7.7
fig:unref-lawlor-qc-dist,lawlor-human-pancreas-smarter.html,7.1
fig:unref-lawlor-qc-comp,lawlor-human-pancreas-smarter.html,7.2
fig:unref-lawlor-norm,lawlor-human-pancreas-smarter.html,7.3
fig:unref-grun-tsne,lawlor-human-pancreas-smarter.html,5.3
lun-416b-cell-line-smart-seq2,lun-416b-cell-line-smart-seq2.html,1
introduction,lun-416b-cell-line-smart-seq2.html,1.1
data-loading,lun-416b-cell-line-smart-seq2.html,1.2
quality-control,lun-416b-cell-line-smart-seq2.html,1.3
normalization,lun-416b-cell-line-smart-seq2.html,1.4
variance-modelling,lun-416b-cell-line-smart-seq2.html,1.5
batch-correction,lun-416b-cell-line-smart-seq2.html,1.6
dimensionality-reduction,lun-416b-cell-line-smart-seq2.html,1.7
clustering,lun-416b-cell-line-smart-seq2.html,1.8
interpretation,lun-416b-cell-line-smart-seq2.html,1.9
fig:unref-416b-qc-dist,lun-416b-cell-line-smart-seq2.html,1.1
fig:unref-416b-qc-comp,lun-416b-cell-line-smart-seq2.html,1.2
fig:unref-416b-norm,lun-416b-cell-line-smart-seq2.html,1.3
fig:unref-416b-variance,lun-416b-cell-line-smart-seq2.html,1.4
fig:unref-416b-tsne,lun-416b-cell-line-smart-seq2.html,1.5
fig:unref-416b-silhouette,lun-416b-cell-line-smart-seq2.html,1.6
fig:unref-416b-markers,lun-416b-cell-line-smart-seq2.html,1.7
messmer-hesc,messmer-hesc.html,13
introduction-12,messmer-hesc.html,13.1
data-loading-12,messmer-hesc.html,13.2
quality-control-12,messmer-hesc.html,13.3
normalization-12,messmer-hesc.html,13.4
cell-cycle-phase-assignment,messmer-hesc.html,13.5
feature-selection,messmer-hesc.html,13.6
batch-correction-1,messmer-hesc.html,13.7
dimensionality-reduction-12,messmer-hesc.html,13.8
fig:unref-messmer-hesc-qc,messmer-hesc.html,13.1
fig:unref-messmer-hesc-norm,messmer-hesc.html,13.2
fig:unref-messmer-hesc-cyclone,messmer-hesc.html,13.3
fig:unref-messmer-hesc-var,messmer-hesc.html,13.4
fig:unref-messmer-hesc-tsne,messmer-hesc.html,13.5
fig:unref-messmer-hesc-cpca-tsne,messmer-hesc.html,13.6
muraro-human-pancreas-cel-seq,muraro-human-pancreas-cel-seq.html,6
introduction-5,muraro-human-pancreas-cel-seq.html,6.1
data-loading-5,muraro-human-pancreas-cel-seq.html,6.2
quality-control-5,muraro-human-pancreas-cel-seq.html,6.3
normalization-5,muraro-human-pancreas-cel-seq.html,6.4
variance-modelling-4,muraro-human-pancreas-cel-seq.html,6.5
data-integration-1,muraro-human-pancreas-cel-seq.html,6.6
dimensionality-reduction-5,muraro-human-pancreas-cel-seq.html,6.7
clustering-5,muraro-human-pancreas-cel-seq.html,6.8
fig:unref-muraro-qc-dist,muraro-human-pancreas-cel-seq.html,6.1
fig:unref-muraro-norm,muraro-human-pancreas-cel-seq.html,6.2
fig:unref-muraro-variance,muraro-human-pancreas-cel-seq.html,6.3
fig:unref-seger-heat,muraro-human-pancreas-cel-seq.html,6.4
fig:unref-muraro-tsne,muraro-human-pancreas-cel-seq.html,6.5
nestorowa-mouse-hsc-smart-seq2,nestorowa-mouse-hsc-smart-seq2.html,10
introduction-9,nestorowa-mouse-hsc-smart-seq2.html,10.1
data-loading-9,nestorowa-mouse-hsc-smart-seq2.html,10.2
quality-control-9,nestorowa-mouse-hsc-smart-seq2.html,10.3
normalization-9,nestorowa-mouse-hsc-smart-seq2.html,10.4
variance-modelling-8,nestorowa-mouse-hsc-smart-seq2.html,10.5
dimensionality-reduction-9,nestorowa-mouse-hsc-smart-seq2.html,10.6
clustering-9,nestorowa-mouse-hsc-smart-seq2.html,10.7
marker-gene-detection-1,nestorowa-mouse-hsc-smart-seq2.html,10.8
cell-type-annotation,nestorowa-mouse-hsc-smart-seq2.html,10.9
miscellaneous-analyses,nestorowa-mouse-hsc-smart-seq2.html,10.10
fig:unref-nest-qc-dist,nestorowa-mouse-hsc-smart-seq2.html,10.1
fig:unref-nest-norm,nestorowa-mouse-hsc-smart-seq2.html,10.2
fig:unref-nest-var,nestorowa-mouse-hsc-smart-seq2.html,10.3
fig:unref-nest-tsne,nestorowa-mouse-hsc-smart-seq2.html,10.4
fig:unref-heat-nest-markers,nestorowa-mouse-hsc-smart-seq2.html,10.5
fig:unref-assignments-nest,nestorowa-mouse-hsc-smart-seq2.html,10.6
fig:unref-nest-facs,nestorowa-mouse-hsc-smart-seq2.html,10.7
paul-mouse-hsc-mars-seq,paul-mouse-hsc-mars-seq.html,11
introduction-10,paul-mouse-hsc-mars-seq.html,11.1
data-loading-10,paul-mouse-hsc-mars-seq.html,11.2
quality-control-10,paul-mouse-hsc-mars-seq.html,11.3
normalization-10,paul-mouse-hsc-mars-seq.html,11.4
variance-modelling-9,paul-mouse-hsc-mars-seq.html,11.5
dimensionality-reduction-10,paul-mouse-hsc-mars-seq.html,11.6
clustering-10,paul-mouse-hsc-mars-seq.html,11.7
fig:unref-paul-qc-dist,paul-mouse-hsc-mars-seq.html,11.1
fig:unref-paul-norm,paul-mouse-hsc-mars-seq.html,11.2
fig:unref-paul-var,paul-mouse-hsc-mars-seq.html,11.3
fig:unref-paul-heat,paul-mouse-hsc-mars-seq.html,11.4
fig:unref-paul-tsne,paul-mouse-hsc-mars-seq.html,11.5
fig:unref-paul-tsne2,paul-mouse-hsc-mars-seq.html,11.6
segerstolpe-human-pancreas-smart-seq2,segerstolpe-human-pancreas-smart-seq2.html,8
introduction-7,segerstolpe-human-pancreas-smart-seq2.html,8.1
data-loading-7,segerstolpe-human-pancreas-smart-seq2.html,8.2
quality-control-7,segerstolpe-human-pancreas-smart-seq2.html,8.3
normalization-7,segerstolpe-human-pancreas-smart-seq2.html,8.4
variance-modelling-6,segerstolpe-human-pancreas-smart-seq2.html,8.5
dimensionality-reduction-7,segerstolpe-human-pancreas-smart-seq2.html,8.6
clustering-7,segerstolpe-human-pancreas-smart-seq2.html,8.7
data-integration-2,segerstolpe-human-pancreas-smart-seq2.html,8.8
segerstolpe-comparison,segerstolpe-human-pancreas-smart-seq2.html,8.9
fig:unref-seger-qc-dist,segerstolpe-human-pancreas-smart-seq2.html,8.1
fig:unref-seger-norm,segerstolpe-human-pancreas-smart-seq2.html,8.2
fig:unref-seger-variance,segerstolpe-human-pancreas-smart-seq2.html,8.3
fig:unref-seger-heat-1,segerstolpe-human-pancreas-smart-seq2.html,8.4
fig:unref-seger-tsne,segerstolpe-human-pancreas-smart-seq2.html,8.5
fig:unref-seger-tsne-correct,segerstolpe-human-pancreas-smart-seq2.html,8.6
fig:unref-ma-plots,segerstolpe-human-pancreas-smart-seq2.html,8.7
fig:unref-voom-plots,segerstolpe-human-pancreas-smart-seq2.html,8.8
unfiltered-human-pbmcs-10x-genomics,unfiltered-human-pbmcs-10x-genomics.html,3
introduction-2,unfiltered-human-pbmcs-10x-genomics.html,3.1
data-loading-2,unfiltered-human-pbmcs-10x-genomics.html,3.2
quality-control-2,unfiltered-human-pbmcs-10x-genomics.html,3.3
normalization-2,unfiltered-human-pbmcs-10x-genomics.html,3.4
variance-modelling-2,unfiltered-human-pbmcs-10x-genomics.html,3.5
dimensionality-reduction-2,unfiltered-human-pbmcs-10x-genomics.html,3.6
clustering-2,unfiltered-human-pbmcs-10x-genomics.html,3.7
interpretation-2,unfiltered-human-pbmcs-10x-genomics.html,3.8
fig:unref-unfiltered-pbmc-qc,unfiltered-human-pbmcs-10x-genomics.html,3.1
fig:unref-unfiltered-pbmc-mito,unfiltered-human-pbmcs-10x-genomics.html,3.2
fig:unref-unfiltered-pbmc-norm,unfiltered-human-pbmcs-10x-genomics.html,3.3
fig:unref-unfiltered-pbmc-var,unfiltered-human-pbmcs-10x-genomics.html,3.4
fig:unref-unfiltered-pbmc-tsne,unfiltered-human-pbmcs-10x-genomics.html,3.5
fig:unref-mono-pbmc-markers,unfiltered-human-pbmcs-10x-genomics.html,3.6
zeisel-mouse-brain-strt-seq,zeisel-mouse-brain-strt-seq.html,2
introduction-1,zeisel-mouse-brain-strt-seq.html,2.1
data-loading-1,zeisel-mouse-brain-strt-seq.html,2.2
quality-control-1,zeisel-mouse-brain-strt-seq.html,2.3
normalization-1,zeisel-mouse-brain-strt-seq.html,2.4
variance-modelling-1,zeisel-mouse-brain-strt-seq.html,2.5
dimensionality-reduction-1,zeisel-mouse-brain-strt-seq.html,2.6
clustering-1,zeisel-mouse-brain-strt-seq.html,2.7
interpretation-1,zeisel-mouse-brain-strt-seq.html,2.8
fig:unref-zeisel-qc-dist,zeisel-mouse-brain-strt-seq.html,2.1
fig:unref-zeisel-qc-comp,zeisel-mouse-brain-strt-seq.html,2.2
fig:unref-zeisel-norm,zeisel-mouse-brain-strt-seq.html,2.3
fig:unref-zeisel-var,zeisel-mouse-brain-strt-seq.html,2.4
fig:unref-zeisel-tsne,zeisel-mouse-brain-strt-seq.html,2.5
fig:unref-zeisel-heat-cell,zeisel-mouse-brain-strt-seq.html,2.6
fig:unref-zeisel-heat-lfc,zeisel-mouse-brain-strt-seq.html,2.7
