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
Software
License: CC BY
Data sources: ZENODO
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
Software . 2025
License: CC BY
Data sources: ZENODO
ZENODO
Software . 2025
License: CC BY
Data sources: Datacite
ZENODO
Software . 2025
License: CC BY
Data sources: Datacite
ZENODO
Software . 2025
License: CC BY
Data sources: Datacite
versions View all 3 versions
addClaim

RareQ: Cell Neighborhood Topology Directs Rare Cell Population Identification

Authors: Fa, Botao;

RareQ: Cell Neighborhood Topology Directs Rare Cell Population Identification

Abstract

RareQ_0.1.0.tar.gz: Source R package of RareQ algorithm for rare cell identification from single-cell data (scRNA-seq, scATAC-seq, CITE-seq) and spatial transcriptomic data (e.g. Xenuim) via neighborhood connectivity (Q)-based network propagation. Tutorial_example.rar: Step-by-step R code for the usage of RareQ in scRNA-seq data, paired scRNA-seq and scATAC-seq data, CITE-seq (RNA and ADT) data, Xenuim spatial data. simulation.rar: Python code and associated datasets for generating simulation datasets in the manuscript. B_lymphoma.rar: Analysis of RareQ in a paired scRNA-seq and scATAC-seq data from human B lymphoma. Source code and data are accompanied. bmcite.rar: Analysis of RareQ in a CITE-seq data in RNA, protein and weighted nearest neighbor (WNN)-integrated data. Source data is RDS format accompanied by R code. Alzheimer.rar: Analysis of RareQ in snRNA-seq data from the brain of healthy and Alzheimer's Disease (AD) patients. Source code and data are accompanied. smFISH.rar: Analysis of RareQ in a spatial transcriptomic data of mouse brain by EEL FISH platform. Source data is h5ad format accompanied by R code. Xenium_Mouse_Brain.rar: Analysis of RareQ in a spatial transcriptomic data of the mouse brain by the Xenium platform. Source code and data are accompanied. Xenium_Human_Kidney_RNA_Protein.rar: Analysis of RareQ in a spatial transcriptomic and protein data of mouse kidney by the Xenium platform. Source code and data are accompanied.

  • 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).
    1
    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!
1
Average
Average
Average