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Classification of low quality cells from single-cell RNA-seq data

Overview of attention for article published in Genome Biology (Online Edition), February 2016
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About this Attention Score

  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (95th percentile)

Mentioned by

news
1 news outlet
blogs
1 blog
twitter
39 tweeters
patent
2 patents
peer_reviews
1 peer review site
wikipedia
1 Wikipedia page
q&a
1 Q&A thread

Citations

dimensions_citation
352 Dimensions

Readers on

mendeley
957 Mendeley
citeulike
7 CiteULike
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Title
Classification of low quality cells from single-cell RNA-seq data
Published in
Genome Biology (Online Edition), February 2016
DOI 10.1186/s13059-016-0888-1
Pubmed ID
Authors

Tomislav Ilicic, Jong Kyoung Kim, Aleksandra A. Kolodziejczyk, Frederik Otzen Bagger, Davis James McCarthy, John C. Marioni, Sarah A. Teichmann

Abstract

Single-cell RNA sequencing (scRNA-seq) has broad applications across biomedical research. One of the key challenges is to ensure that only single, live cells are included in downstream analysis, as the inclusion of compromised cells inevitably affects data interpretation. Here, we present a generic approach for processing scRNA-seq data and detecting low quality cells, using a curated set of over 20 biological and technical features. Our approach improves classification accuracy by over 30 % compared to traditional methods when tested on over 5,000 cells, including CD4+ T cells, bone marrow dendritic cells, and mouse embryonic stem cells.

Twitter Demographics

The data shown below were collected from the profiles of 39 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 957 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 7 <1%
Japan 3 <1%
Sweden 2 <1%
Denmark 2 <1%
United States 2 <1%
Spain 1 <1%
Egypt 1 <1%
Taiwan 1 <1%
Unknown 938 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 249 26%
Researcher 201 21%
Student > Master 110 11%
Student > Bachelor 100 10%
Student > Doctoral Student 50 5%
Other 115 12%
Unknown 132 14%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 284 30%
Agricultural and Biological Sciences 235 25%
Medicine and Dentistry 54 6%
Neuroscience 51 5%
Immunology and Microbiology 51 5%
Other 118 12%
Unknown 164 17%

Attention Score in Context

This research output has an Altmetric Attention Score of 45. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 23 September 2021.
All research outputs
#652,935
of 19,814,211 outputs
Outputs from Genome Biology (Online Edition)
#531
of 3,874 outputs
Outputs of similar age
#13,576
of 275,771 outputs
Outputs of similar age from Genome Biology (Online Edition)
#1
of 1 outputs
Altmetric has tracked 19,814,211 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 96th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,874 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 26.9. This one has done well, scoring higher than 86% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 275,771 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 95% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them