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7821791
create tutorial.md using scrna-seurat-pbmc3k as template
kevinrue Jul 3, 2026
cb2daaa
declare R libraries used
kevinrue Jul 3, 2026
778562c
copy data upload section from seurat
kevinrue Jul 3, 2026
a292ea8
add read10Xcounts step
kevinrue Jul 3, 2026
4a693c8
small edits
kevinrue Jul 4, 2026
1631860
add context to sce objects
kevinrue Jul 4, 2026
e036d77
fix gtn links
kevinrue Jul 5, 2026
d1c4947
add a section about displaying the sce object
kevinrue Jul 5, 2026
169d44e
add explanations
kevinrue Jul 5, 2026
111ba87
do not skip a heading level
kevinrue Jul 5, 2026
f3f7d80
add identification of mitochondrial genes and calculation of quality …
kevinrue Jul 6, 2026
2e8ad8b
extend the tutorial up to the calculation of quality control metrics
kevinrue Jul 6, 2026
a682fe2
reorder text
kevinrue Jul 6, 2026
9ad55f9
highlight code and comments with appropriate markup
kevinrue Jul 6, 2026
eee74ba
apply markup until the end of the tutorial so far
kevinrue Jul 6, 2026
8afca20
add mention of separate scater tutorial as reference
kevinrue Jul 6, 2026
5b6ac9c
extend tutorial to inspection and visualisation of qc metrics
kevinrue Jul 8, 2026
be5aee4
additional use case for plotColData
kevinrue Jul 8, 2026
43a1e8f
Merge branch 'main' into kra-scrnaseq-bioc-pbmc3k
kevinrue Jul 8, 2026
90fe3e9
add images of expected plots
kevinrue Jul 8, 2026
dc5a410
plotColData needs to be called once per combination of x-y features
kevinrue Jul 8, 2026
a9a7040
filter out low quality cells
kevinrue Jul 14, 2026
7e51909
expand tutorial to visualisation of qc metrics after filtering
kevinrue Jul 14, 2026
0b9aacd
update tutorial to logNormCounts
kevinrue Jul 15, 2026
0cbf3e0
extend tutorial to modelling of gene variance
kevinrue Jul 15, 2026
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Original file line number Diff line number Diff line change
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@article{amezquita2019orchestrating,
title={Orchestrating Single-Cell Analysis with Bioconductor},
author={Amezquita, Robert A and Carey, Vince J and Carpp, Lindsay N and Geistlinger, Ludwig and Lun, Aaron TL and Marini, Federico and Rue-Albrecht, Kevin and Risso, Davide and Soneson, Charlotte and Waldron, Levi and others},
journal={bioRxiv},
pages={590562},
year={2019},
publisher={Cold Spring Harbor Laboratory},
url={https://www.biorxiv.org/content/10.1101/590562v1}
}
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