QClus: a droplet filtering algorithm for enhanced snRNA-seq data quality in challenging samples Article Swipe
Eloi Schmauch
,
Johannes Ojanen
,
Kyriakitsa Galani
,
Juho Jalkanen
,
Kristiina Harju
,
Maija Hollmén
,
Hannu Kokki
,
Jarmo Gunn
,
Jari Halonen
,
Juha Hartikainen
,
Tuomas Kiviniemi
,
Pasi Tavi
,
Minna U. Kaikkonen
,
Manolis Kellis
,
Suvi Linna-Kuosmanen
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkae1145
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkae1145
Single-nuclei RNA sequencing remains a challenge for many human tissues, as incomplete removal of background signal masks cell-type-specific signals and interferes with downstream analyses. Here, we present Quality Clustering (QClus), a droplet filtering algorithm targeted toward challenging samples. QClus uses additional metrics, such as cell-type-specific marker gene expression, to cluster nuclei and filter empty and highly contaminated droplets, providing reliable filtering of samples with varying number of nuclei and contamination levels. In a benchmarking analysis against seven alternative methods across six datasets, consisting of 252 samples and over 1.9 million nuclei, QClus achieved the highest quality in the greatest number of samples over all evaluated quality metrics and recorded no processing failures, while robustly retaining numbers of nuclei within the expected range. QClus combines high quality, automation and robustness with flexibility and user-adjustability, catering to diverse experimental needs and datasets.
Related Topics
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/nar/gkae1145
- https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkae1145/60958101/gkae1145.pdf
- OA Status
- gold
- Cited By
- 2
- References
- 37
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4405228508
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4405228508Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/nar/gkae1145Digital Object Identifier
- Title
-
QClus: a droplet filtering algorithm for enhanced snRNA-seq data quality in challenging samplesWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-11-04Full publication date if available
- Authors
-
Eloi Schmauch, Johannes Ojanen, Kyriakitsa Galani, Juho Jalkanen, Kristiina Harju, Maija Hollmén, Hannu Kokki, Jarmo Gunn, Jari Halonen, Juha Hartikainen, Tuomas Kiviniemi, Pasi Tavi, Minna U. Kaikkonen, Manolis Kellis, Suvi Linna-KuosmanenList of authors in order
- Landing page
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https://doi.org/10.1093/nar/gkae1145Publisher landing page
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https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkae1145/60958101/gkae1145.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkae1145/60958101/gkae1145.pdfDirect OA link when available
- Concepts
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Biology, Algorithm, Computational biology, Computer scienceTop concepts (fields/topics) attached by OpenAlex
- Cited by
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2Total citation count in OpenAlex
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2025: 2Per-year citation counts (last 5 years)
- References (count)
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37Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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