Cargando…

scIBD: a self-supervised iterative-optimizing model for boosting the detection of heterotypic doublets in single-cell chromatin accessibility data

Application of the widely used droplet-based microfluidic technologies in single-cell sequencing often yields doublets, introducing bias to downstream analyses. Especially, doublet-detection methods for single-cell chromatin accessibility sequencing (scCAS) data have multiple assay-specific challeng...

Descripción completa

Detalles Bibliográficos
Autores principales:	Zhang, Wenhao, Jiang, Rui, Chen, Shengquan, Wang, Ying
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2023
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10561408/ https://www.ncbi.nlm.nih.gov/pubmed/37814314 http://dx.doi.org/10.1186/s13059-023-03072-y

Ejemplares similares

Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG
por: Duren, Zhana, et al.
Publicado: (2022)

geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq
por: Missarova, Alsu, et al.
Publicado: (2021)

scROSHI: robust supervised hierarchical identification of single cells
por: Prummer, Michael, et al.
Publicado: (2023)

scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data
por: Alquicira-Hernandez, Jose, et al.
Publicado: (2019)

scDemultiplex: An iterative beta-binomial model-based method for accurate demultiplexing with hashtag oligos
por: Huang, Li-Ching, et al.
Publicado: (2023)

Stability of scRNA-Seq Analysis Workflows is Susceptible to Preprocessing and is Mitigated by Regularized or Supervised Approaches
por: Durmaz, Arda, et al.
Publicado: (2022)

methyl-ATAC-seq measures DNA methylation at accessible chromatin
por: Spektor, Roman, et al.
Publicado: (2019)

Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility
por: Xing, Qiao Rui, et al.
Publicado: (2020)

MEDEA: analysis of transcription factor binding motifs in accessible chromatin
por: Mariani, Luca, et al.
Publicado: (2020)

Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples
por: Zhang, Hua, et al.
Publicado: (2022)

Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics
por: Stoeckius, Marlon, et al.
Publicado: (2018)

A synergistic DNA logic predicts genome-wide chromatin accessibility
por: Hashimoto, Tatsunori, et al.
Publicado: (2016)

APEC: an accesson-based method for single-cell chromatin accessibility analysis
por: Li, Bin, et al.
Publicado: (2020)

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells
por: Miraldi, Emily R., et al.
Publicado: (2019)

TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence
por: Ouyang, Ningxin, et al.
Publicado: (2020)

Time course regulatory analysis based on paired expression and chromatin accessibility data
por: Duren, Zhana, et al.
Publicado: (2020)

DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility
por: Liu, Qiao, et al.
Publicado: (2022)

scDART: integrating unmatched scRNA-seq and scATAC-seq data and learning cross-modality relationship simultaneously
por: Zhang, Ziqi, et al.
Publicado: (2022)

Dynamic chromatin accessibility deploys heterotypic cis/trans-acting factors driving stomatal cell-fate commitment
por: Kim, Eun-Deok, et al.
Publicado: (2022)

Optimization of the Omni-ATAC protocol to chromatin accessibility profiling in snap-frozen rat adipose and muscle tissues
por: Nair, Venugopalan D., et al.
Publicado: (2022)

Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay
por: Sos, Brandon Chin, et al.
Publicado: (2016)

Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning
por: Atak, Zeynep Kalender, et al.
Publicado: (2021)

Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing
por: O'Connell, Brendan L., et al.
Publicado: (2023)

Iterative epigenomic analyses in the same single cell
por: Ohnuki, Hidetaka, et al.
Publicado: (2021)

Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data
por: Luo, Kaixuan, et al.
Publicado: (2022)

BindVAE: Dirichlet variational autoencoders for de novo motif discovery from accessible chromatin
por: Kshirsagar, Meghana, et al.
Publicado: (2022)

Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay
por: Hammelman, Jennifer, et al.
Publicado: (2020)

Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumors
por: Marcel, Shelsa S., et al.
Publicado: (2021)

scAlign: a tool for alignment, integration, and rare cell identification from scRNA-seq data
por: Johansen, Nelson, et al.
Publicado: (2019)

scEMAIL: Universal and Source-free Annotation Method for scRNA-seq Data with Novel Cell-type Perception
por: Wan, Hui, et al.
Publicado: (2022)

Modulating chromatin accessibility by transactivation and targeting proximal dsgRNAs enhances Cas9 editing efficiency in vivo
por: Liu, Guanwen, et al.
Publicado: (2019)

Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data
por: Qin, Qian, et al.
Publicado: (2020)

ATAC-STARR-seq reveals transcription factor–bound activators and silencers within chromatin-accessible regions of the human genome
por: Hansen, Tyler J., et al.
Publicado: (2022)

Doublet identification in single-cell sequencing data using scDblFinder
por: Germain, Pierre-Luc, et al.
Publicado: (2022)

Cell type-specific interaction analysis using doublets in scRNA-seq
por: Schiebout, Courtney, et al.
Publicado: (2023)

TIGRA: A targeted iterative graph routing assembler for breakpoint assembly
por: Chen, Ken, et al.
Publicado: (2014)

I-Boost: an integrative boosting approach for predicting survival time with multiple genomics platforms
por: Wong, Kin Yau, et al.
Publicado: (2019)

RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts
por: Naseri, Ardalan, et al.
Publicado: (2019)

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
por: Tsai, Isheng J, et al.
Publicado: (2010)

Genealogical inference and more flexible sequence clustering using iterative-PopPUNK
por: Zhao, Bin, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_87j5q8jj9konfltuk83ov7i92l