Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes

Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes

Abstract Background RNA profiling technologies at single-cell resolutions, including single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq, scnRNA-seq for short), can help characterize the composition of tissues and reveal cells that influence key functions in both healthy and diseas...

Full description

Bibliographic Details
Main Authors:	Francisco Avila Cobos, Mohammad Javad Najaf Panah, Jessica Epps, Xiaochen Long, Tsz-Kwong Man, Hua-Sheng Chiu, Elad Chomsky, Evgeny Kiner, Michael J. Krueger, Diego di Bernardo, Luis Voloch, Jan Molenaar, Sander R. van Hooff, Frank Westermann, Selina Jansky, Michele L. Redell, Pieter Mestdagh, Pavel Sumazin
Format:	Article
Language:	English
Published:	BMC 2023-08-01
Series:	Genome Biology
Online Access:	https://doi.org/10.1186/s13059-023-03016-6

Similar Items

An Efficient and Flexible Method for Deconvoluting Bulk RNA-Seq Data with Single-Cell RNA-Seq Data
by: Xifang Sun, et al.
Published: (2019-09-01)

Unraveling the complexity: understanding the deconvolutions of RNA-seq data
by: Kavoos Momeni, et al.
Published: (2023-09-01)

HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD)
by: Yen-Jung Chiu, et al.
Published: (2023-10-01)

Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq
by: Giulia Biancon, et al.
Published: (2022-12-01)

Digitaldlsorter: Deep-Learning on scRNA-Seq to Deconvolute Gene Expression Data
by: Carlos Torroja, et al.
Published: (2019-10-01)

A benchmark for RNA-seq deconvolution analysis under dynamic testing environments
by: Haijing Jin, et al.
Published: (2021-04-01)

Corrigendum: Digitaldlsorter: Deep-Learning on scRNA-Seq to Deconvolute Gene Expression Data
by: Carlos Torroja, et al.
Published: (2020-02-01)

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data
by: Francesca Finotello, et al.
Published: (2019-05-01)

Resolving host-pathogen interactions by dual RNA-seq.
by: Alexander J Westermann, et al.
Published: (2017-02-01)

Correction to: Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data
by: Francesca Finotello, et al.
Published: (2019-07-01)

ScRNA-seq and ST-seq in liver research
by: Jia He, et al.
Published: (2023-02-01)

SeqOthello: querying RNA-seq experiments at scale
by: Ye Yu, et al.
Published: (2018-10-01)

SCRABBLE: single-cell RNA-seq imputation constrained by bulk RNA-seq data
by: Tao Peng, et al.
Published: (2019-05-01)

Deciphering Tumour Microenvironment of Liver Cancer through Deconvolution of Bulk RNA-Seq Data with Single-Cell Atlas
by: Shaoshi Zhang, et al.
Published: (2022-12-01)

EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data
by: Andrew E. Teschendorff, et al.
Published: (2020-09-01)

Integrating RNA-seq and scRNA-seq to explore the mechanism of macrophage ferroptosis associated with COPD
by: Pengbei Fan, et al.
Published: (2023-03-01)

Interactive Analysis, Exploration, and Visualization of RNA-Seq Data with SeqCVIBE
by: Efthimios Bothos, et al.
Published: (2022-03-01)

Massively parallel single-nucleus RNA-seq with DroNc-seq
by: Avraham-Davidi, Inbal, et al.
Published: (2018)

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification
by: Tamar Hashimshony, et al.
Published: (2012-09-01)

Giardia lamblia transcriptome analysis using TSS-Seq and RNA-Seq.
by: Mohammed E M Tolba, et al.
Published: (2013-01-01)

Gene mapping via bulked segregant RNA-Seq (BSR-Seq).
by: Sanzhen Liu, et al.
Published: (2012-01-01)

MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions
by: Yael Baran, et al.
Published: (2019-10-01)

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)

Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data
by: Amit Blumberg, et al.
Published: (2021-02-01)

Discovery of protein-lncRNA interactions by integrating large-scale CLIP-Seq and RNA-Seq datasets
by: Jun-Hao eLi, et al.
Published: (2015-01-01)

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
by: MacIntosh Cornwell, et al.
Published: (2018-04-01)

A Deconvolution Protocol for ChIP-Seq Reveals Analogous Enhancer Structures on the Mouse and Human Ribosomal RNA Genes
by: Jean-Clement Mars, et al.
Published: (2018-01-01)

RNA-seq: impact of RNA degradation on transcript quantification
by: Gallego Romero, Irene, et al.
Published: (2015)

Exploring PANoptosis in breast cancer based on scRNA-seq and bulk-seq
by: Puxing He, et al.
Published: (2023-06-01)

Investigation of the effects of phthalates on in vitro thyroid models with RNA-Seq and ATAC-Seq
by: Marta Nazzari, et al.
Published: (2023-09-01)

Integration of ATAC-Seq and RNA-Seq identifies the key genes in myocardial ischemia
by: Jing Yuan, et al.
Published: (2023-01-01)

The Vacc-SeqQC project: Benchmarking RNA-Seq for clinical vaccine studies
by: Johannes B. Goll, et al.
Published: (2023-01-01)

CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq
by: Hashimshony, Tamar, et al.
Published: (2016)

COEX-Seq: Convert a Variety of Measurements of Gene Expression in RNA-Seq
by: Sang Cheol Kim, et al.
Published: (2018-12-01)

RNA-seq transcriptional atlas for the rat
by: Bush, S
Published: (2021)

Revealing the History and Mystery of RNA-Seq
by: Aishwarya Gondane, et al.
Published: (2023-02-01)

Development and evaluation of RNA-seq methods
by: Levin, Joshua Z., et al.
Published: (2012)

RNA-seq: technical variability and sampling
by: Oberg Ann L, et al.
Published: (2011-06-01)

RNA-seq assembly – Are we there yet?
by: Simon eSchliesky, et al.
Published: (2012-09-01)

Integration of scRNA-Seq and Bulk RNA-Seq Reveals Molecular Characterization of the Immune Microenvironment in Acute Pancreatitis
by: Zhen Fang, et al.
Published: (2022-12-01)