M3S: a comprehensive model selection for multi-modal single-cell RNA sequencing data

M3S: a comprehensive model selection for multi-modal single-cell RNA sequencing data

Abstract Background Various statistical models have been developed to model the single cell RNA-seq expression profiles, capture its multimodality, and conduct differential gene expression test. However, for expression data generated by different experimental design and platforms, there is currently...

Full description

Bibliographic Details
Main Authors:	Yu Zhang, Changlin Wan, Pengcheng Wang, Wennan Chang, Yan Huo, Jian Chen, Qin Ma, Sha Cao, Chi Zhang
Format:	Article
Language:	English
Published:	BMC 2019-12-01
Series:	BMC Bioinformatics
Subjects:	Single cell RNA-seq Multimodality Differential gene expression analysis Drop-seq Left truncated mixture Gaussian
Online Access:	https://doi.org/10.1186/s12859-019-3243-1

Similar Items

The effect of methanol fixation on single-cell RNA sequencing data
by: Xinlei Wang, et al.
Published: (2021-06-01)

scAPAmod: Profiling Alternative Polyadenylation Modalities in Single Cells from Single-Cell RNA-Seq Data
by: Lingwu Qian, et al.
Published: (2022-07-01)

Supplemental Tables for Comprehensive single-cell transcriptional profiling of the regenerative planarian Schmidtea mediterranea
by: Fincher, Christopher T., et al.
Published: (2020)

Recommendations of scRNA-seq Differential Gene Expression Analysis Based on Comprehensive Benchmarking
by: Jake Gagnon, et al.
Published: (2022-06-01)

Improved protocol for single-nucleus RNA-sequencing of frozen human bladder tumor biopsies
by: Sofie S. Schmøkel, et al.
Published: (2023-12-01)

Dual indexed library design enables compatibility of in-Drop single-cell RNA-sequencing with exAMP chemistry sequencing platforms
by: Austin N. Southard-Smith, et al.
Published: (2020-07-01)

Single-cell RNA-seq analysis of the brainstem of mutant SOD1 mice reveals perturbed cell types and pathways of amyotrophic lateral sclerosis
by: Wenting Liu, et al.
Published: (2020-07-01)

FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5′-end single-cell RNA sequencing
by: Yun Li, et al.
Published: (2023-04-01)

Evaluation of STAR and Kallisto on Single Cell RNA-Seq Data Alignment
by: Yuheng Du, et al.
Published: (2020-05-01)

BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks
by: Lorinc S. Pongor, et al.
Published: (2020-04-01)

GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership
by: Peter Carbonetto, et al.
Published: (2023-10-01)

Prognostic assessment capability of a five-gene signature in pancreatic cancer: a machine learning based-study
by: Xuanfeng Zhang, et al.
Published: (2023-03-01)

Protocol for nuclear dissociation of the adult C. elegans for single-nucleus RNA sequencing and its application for mapping environmental responses
by: Max T. Levenson, et al.
Published: (2023-12-01)

Exploring the cellular and molecular differences between ovarian clear cell carcinoma and high-grade serous carcinoma using single-cell RNA sequencing and GEO gene expression signatures
by: Dan Guo, et al.
Published: (2023-07-01)

Decontamination of ambient RNA in single-cell RNA-seq with DecontX
by: Shiyi Yang, et al.
Published: (2020-03-01)

A statistical approach for identifying primary substrates of ZSWIM8-mediated microRNA degradation in small-RNA sequencing data
by: Peter Y. Wang, et al.
Published: (2023-05-01)

Defining the Transcriptional Landscape during Cytomegalovirus Latency with Single-Cell RNA Sequencing
by: Miri Shnayder, et al.
Published: (2018-05-01)

CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction
by: Carlos Guzman, et al.
Published: (2017-08-01)

Subject level clustering using a negative binomial model for small transcriptomic studies
by: Qian Li, et al.
Published: (2018-12-01)

scDART: integrating unmatched scRNA-seq and scATAC-seq data and learning cross-modality relationship simultaneously
by: Ziqi Zhang, et al.
Published: (2022-06-01)

Comparison of Single Cell Transcriptome Sequencing Methods: Of Mice and Men
by: Bastian V. H. Hornung, et al.
Published: (2023-12-01)

DNA methylome profiling at single-base resolution through bisulfite sequencing of 5mC-immunoprecipitated DNA
by: Zhen Jia, et al.
Published: (2018-02-01)

Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data
by: Jordan Sicherman, et al.
Published: (2021-03-01)

Accounting for cell type hierarchy in evaluating single cell RNA-seq clustering
by: Zhijin Wu, et al.
Published: (2020-05-01)

Epi-Impute: Single-Cell RNA-seq Imputation via Integration with Single-Cell ATAC-seq
by: Mikhail Raevskiy, et al.
Published: (2023-03-01)

Methods, Challenges and Potentials of Single Cell RNA-seq
by: Daniel Hebenstreit
Published: (2012-11-01)

scGMM-VGAE: a Gaussian mixture model-based variational graph autoencoder algorithm for clustering single-cell RNA-seq data
by: Eric Lin, et al.
Published: (2023-01-01)

Cell fixation and preservation for droplet-based single-cell transcriptomics
by: Jonathan Alles, et al.
Published: (2017-05-01)

Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods
by: Alessandra Dal Molin, et al.
Published: (2017-05-01)

Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice
by: Wendi A. Bacon, et al.
Published: (2018-11-01)

A comparison between whole transcript and 3’ RNA sequencing methods using Kapa and Lexogen library preparation methods
by: Feiyang Ma, et al.
Published: (2019-01-01)

Leveraging Novel Integrated Single-Cell Analyses to Define HIV-1 Latency Reversal
by: Suhui Zhao, et al.
Published: (2021-06-01)

Correcting nucleotide-specific biases in high-throughput sequencing data
by: Jeremy R. Wang, et al.
Published: (2017-08-01)

Estimating the frequency of multiplets in single-cell RNA sequencing from cell-mixing experiments
by: Jesse D. Bloom
Published: (2018-09-01)

Integrative single-cell analysis of cardiac and pulmonary sarcoidosis using publicly available cardiac and bronchoalveolar lavage fluid sequencing datasets
by: Abdel Daoud, et al.
Published: (2023-07-01)

Uncovering Hidden Factors in Electricity Consumption Based on Gaussian Mixture Estimation
by: Shiwen Liao, et al.
Published: (2022-01-01)

The shaky foundations of simulating single-cell RNA sequencing data
by: Helena L. Crowell, et al.
Published: (2023-03-01)

Comparative Toxicotranscriptomics of Single Cell RNA-Seq and Conventional RNA-Seq in TCDD-Exposed Testicular Tissue
by: Alex Haimbaugh, et al.
Published: (2022-05-01)

Reconstruction of the Global Polarity of an Early Spider Embryo by Single-Cell and Single-Nucleus Transcriptome Analysis
by: Yasuko Akiyama-Oda, et al.
Published: (2022-07-01)

The Construction and Exploration of a Comprehensive MicroRNA Centered Regulatory Network in Foxtail Millet (Setaria italica L.)
by: Yang Deng, et al.
Published: (2022-05-01)