Cargando…

Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity

Methods for cell clustering and gene expression from single-cell RNA sequencing (scRNA-seq) data are essential for biological interpretation of cell processes. Here, we present TRIAGE-Cluster which uses genome-wide epigenetic data from diverse bio-samples to identify genes demarcating cell diversity...

Descripción completa

Detalles Bibliográficos
Autores principales:	Sun, Yuliangzi, Shim, Woo Jun, Shen, Sophie, Sinniah, Enakshi, Pham, Duy, Su, Zezhuo, Mizikovsky, Dalia, White, Melanie D, Ho, Joshua W K, Nguyen, Quan, Bodén, Mikael, Palpant, Nathan J
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2023
Materias:	Methods Online
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10287941/ https://www.ncbi.nlm.nih.gov/pubmed/37125641 http://dx.doi.org/10.1093/nar/gkad307

Ejemplares similares

Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity
por: Shim, Woo Jun, et al.
Publicado: (2020)

Organization of gene programs revealed by unsupervised analysis of diverse gene–trait associations
por: Mizikovsky, Dalia, et al.
Publicado: (2022)

CellDART: cell type inference by domain adaptation of single-cell and spatial transcriptomic data
por: Bae, Sungwoo, et al.
Publicado: (2022)

Cell lineage inference from SNP and scRNA-Seq data
por: Ding, Jun, et al.
Publicado: (2019)

Single-cell gene regulation network inference by large-scale data integration
por: Dong, Xin, et al.
Publicado: (2022)

CisMapper: predicting regulatory interactions from transcription factor ChIP-seq data
por: O'Connor, Timothy, et al.
Publicado: (2017)

Inferring short tandem repeat variation from paired-end short reads
por: Cao, Minh Duc, et al.
Publicado: (2014)

Inferring transcription factor complexes from ChIP-seq data
por: Whitington, Tom, et al.
Publicado: (2011)

Inference of cell state transitions and cell fate plasticity from single-cell with MARGARET
por: Pandey, Kushagra, et al.
Publicado: (2022)

Cell lineage and communication network inference via optimization for single-cell transcriptomics
por: Wang, Shuxiong, et al.
Publicado: (2019)

Inference of Relationships in Population Data Using Identity-by-Descent and Identity-by-State
por: Stevens, Eric L., et al.
Publicado: (2011)

SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics
por: Cabello-Aguilar, Simon, et al.
Publicado: (2020)

Cell-specific network constructed by single-cell RNA sequencing data
por: Dai, Hao, et al.
Publicado: (2019)

A transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification
por: Plaisance, Isabelle, et al.
Publicado: (2022)

HapFABIA: Identification of very short segments of identity by descent characterized by rare variants in large sequencing data
por: Hochreiter, Sepp
Publicado: (2013)

NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types
por: Lee, Sejoon, et al.
Publicado: (2017)

Integration of single cell data by disentangled representation learning
por: Guo, Tiantian, et al.
Publicado: (2021)

Integrated analysis of multimodal single-cell data with structural similarity
por: Cao, Yingxin, et al.
Publicado: (2022)

Using single cell atlas data to reconstruct regulatory networks
por: Song, Qi, et al.
Publicado: (2023)

Reconstructing physical cell interaction networks from single-cell data using Neighbor-seq
por: Ghaddar, Bassel, et al.
Publicado: (2022)

Robust lineage reconstruction from high-dimensional single-cell data
por: Giecold, Gregory, et al.
Publicado: (2016)

RUV-III-NB: normalization of single cell RNA-seq data
por: Salim, Agus, et al.
Publicado: (2022)

CT-FOCS: a novel method for inferring cell type-specific enhancer–promoter maps
por: Hait, Tom Aharon, et al.
Publicado: (2022)

CellBIC: bimodality-based top-down clustering of single-cell RNA sequencing data reveals hierarchical structure of the cell type
por: Kim, Junil, et al.
Publicado: (2018)

Cytocipher determines significantly different populations of cells in single-cell RNA-seq data
por: Balderson, Brad, et al.
Publicado: (2023)

Detecting critical transition signals from single-cell transcriptomes to infer lineage-determining transcription factors
por: Yang, Xinan H, et al.
Publicado: (2022)

Linnorm: improved statistical analysis for single cell RNA-seq expression data
por: Yip, Shun H., et al.
Publicado: (2017)

Network embedding-based representation learning for single cell RNA-seq data
por: Li, Xiangyu, et al.
Publicado: (2017)

Using neural networks for reducing the dimensions of single-cell RNA-Seq data
por: Lin, Chieh, et al.
Publicado: (2017)

Computational identification of cell-specific variable regions in ChIP-seq data
por: Andreani, Tommaso, et al.
Publicado: (2020)

Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data
por: Reed, Eric R, et al.
Publicado: (2021)

A sparse differential clustering algorithm for tracing cell type changes via single-cell RNA-sequencing data
por: Barron, Martin, et al.
Publicado: (2018)

Effective and scalable single-cell data alignment with non-linear canonical correlation analysis
por: Hu, Jialu, et al.
Publicado: (2021)

MARVEL: an integrated alternative splicing analysis platform for single-cell RNA sequencing data
por: Wen, Wei Xiong, et al.
Publicado: (2023)

exFINDER: identify external communication signals using single-cell transcriptomics data
por: He, Changhan, et al.
Publicado: (2023)

Leveraging Identity-by-Descent for Accurate Genotype Inference in Family Sequencing Data
por: Li, Bingshan, et al.
Publicado: (2015)

Simplified RNA secondary structure mapping by automation of SHAPE data analysis
por: Pang, Phillip S., et al.
Publicado: (2011)

Inferring regulators of cell identity in the human adult pancreas
por: Vanheer, Lotte, et al.
Publicado: (2023)

Tree inference for single-cell data
por: Jahn, Katharina, et al.
Publicado: (2016)

Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data
por: Nakajima, Natsu, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_e4pc8761k2003rqe4btr5mg4ff