Powered by OpenAIRE graph
Found an issue? Give us feedback
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
ZENODO
Dataset . 2024
Data sources: ZENODO
ZENODO
Dataset . 2024
Data sources: Datacite
versions View all 1 versions
addClaim

Supplementary Material for the paper entitled "Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data"

Authors: Crawford, Lorin;

Supplementary Material for the paper entitled "Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data"

Abstract

This repo contain supplementary tables from the manuscript entitled: "Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data". Clustering is a common way to identify cell types in single-cell RNA-sequencing (scRNA-seq) data. Unfortunately, current methods (i) require users to make human-in-the-loop decisions, which adds significant runtime to bioinformatic analyses, and (ii) reuse the same data twice when testing for differentially expressed genes, which can lead to an increased number of false discoveries. In this work, we overcome these limitations with NCLUSION: a Bayesian nonparametric method that simultaneously clusters cells and selects marker genes. NCLUSION operates without user-defined heuristics to set model parameters and leverages variational expectation-maximization (EM) for posterior inference which allows it to scale well up to 1 million cells. By analyzing publicly available datasets, we illustrate that NCLUSION matches the state-of-the-art clustering performance of competing approaches, achieves improved computational efficiency, and directly enables identification of biologically relevant gene sets driving cluster definitions.

Related Organizations
  • BIP!
    Impact byBIP!
    selected citations
    These citations are derived from selected sources.
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    0
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Average
Powered by OpenAIRE graph
Found an issue? Give us feedback
selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average