Cargando…

scMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens

We present scMAGeCK, a computational framework to identify genomic elements associated with multiple expression-based phenotypes in CRISPR/Cas9 functional screening that uses single-cell RNA-seq as readout. scMAGeCK outperforms existing methods, identifies genes and enhancers with known and novel fu...

Descripción completa

Detalles Bibliográficos
Autores principales:	Yang, Lin, Zhu, Yuqing, Yu, Hua, Cheng, Xiaolong, Chen, Sitong, Chu, Yulan, Huang, He, Zhang, Jin, Li, Wei
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2020
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6979386/ https://www.ncbi.nlm.nih.gov/pubmed/31980032 http://dx.doi.org/10.1186/s13059-020-1928-4

Ejemplares similares

Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR
por: Li, Wei, et al.
Publicado: (2015)

MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens
por: Li, Wei, et al.
Publicado: (2014)

Direct-seq: programmed gRNA scaffold for streamlined scRNA-seq in CRISPR screen
por: Song, Qingkai, et al.
Publicado: (2020)

CRMAGE: CRISPR Optimized MAGE Recombineering
por: Ronda, Carlotta, et al.
Publicado: (2016)

A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening
por: Diao, Yarui, et al.
Publicado: (2016)

gscreend: modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection
por: Imkeller, Katharina, et al.
Publicado: (2020)

Large‐scale image‐based profiling of single‐cell phenotypes in arrayed CRISPR‐Cas9 gene perturbation screens
por: de Groot, Reinoud, et al.
Publicado: (2018)

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

scLink: Inferring Sparse Gene Co-expression Networks from Single-cell Expression Data
por: Li, Wei Vivian, et al.
Publicado: (2021)

CRISPR/Cas9 screening using unique molecular identifiers
por: Schmierer, Bernhard, et al.
Publicado: (2017)

JACKS: joint analysis of CRISPR/Cas9 knockout screens
por: Allen, Felicity, et al.
Publicado: (2019)

Guide RNAs with embedded barcodes boost CRISPR-pooled screens
por: Zhu, Shiyou, et al.
Publicado: (2019)

MAUDE: inferring expression changes in sorting-based CRISPR screens
por: de Boer, Carl G., et al.
Publicado: (2020)

A solid‐phase transfection platform for arrayed CRISPR screens
por: Serçin, Özdemirhan, et al.
Publicado: (2019)

CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes
por: Rossato, Marzia, et al.
Publicado: (2023)

High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9
por: Varshney, Gaurav K., et al.
Publicado: (2015)

CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens
por: Daley, Timothy P., et al.
Publicado: (2018)

Pooled extracellular receptor-ligand interaction screening using CRISPR activation
por: Chong, Zheng-Shan, et al.
Publicado: (2018)

SCEPTRE improves calibration and sensitivity in single-cell CRISPR screen analysis
por: Barry, Timothy, 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)

Dimensionality reduction methods for extracting functional networks from large‐scale CRISPR screens
por: Hassan, Arshia Zernab, et al.
Publicado: (2023)

scClassify: sample size estimation and multiscale classification of cells using single and multiple reference
por: Lin, Yingxin, et al.
Publicado: (2020)

scMC learns biological variation through the alignment of multiple single-cell genomics datasets
por: Zhang, Lihua, et al.
Publicado: (2021)

scLM: Automatic Detection of Consensus Gene Clusters Across Multiple Single-cell Datasets
por: Song, Qianqian, et al.
Publicado: (2021)

GEMINI: a variational Bayesian approach to identify genetic interactions from combinatorial CRISPR screens
por: Zamanighomi, Mahdi, et al.
Publicado: (2019)

In situ genotyping of a pooled strain library after characterizing complex phenotypes
por: Lawson, Michael J, et al.
Publicado: (2017)

Arrayed CRISPR screen with image-based assay reliably uncovers host genes required for coxsackievirus infection
por: Kim, Heon Seok, et al.
Publicado: (2018)

DeepCRISPR: optimized CRISPR guide RNA design by deep learning
por: Chuai, Guohui, et al.
Publicado: (2018)

CIGAR‐seq, a CRISPR/Cas‐based method for unbiased screening of novel mRNA modification regulators
por: Fang, Liang, et al.
Publicado: (2020)

CRISPR‐TAPE: protein‐centric CRISPR guide design for targeted proteome engineering
por: Anderson, Daniel Paolo, et al.
Publicado: (2020)

Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives
por: Jeong, Hyun-Hwan, et al.
Publicado: (2019)

Genome-wide CRISPR screening reveals genes essential for cell viability and resistance to abiotic and biotic stresses in Bombyx mori
por: Chang, Jiasong, et al.
Publicado: (2020)

CRISPR-edit point mutant allele detection (CEPAD)-PCR method for rapid screening of CRISPR edited point mutations
por: Trimmer, Kenneth, et al.
Publicado: (2021)

scSorter: assigning cells to known cell types according to marker genes
por: Guo, Hongyu, et al.
Publicado: (2021)

scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution
por: Kapourani, Chantriolnt-Andreas, et al.
Publicado: (2021)

PWAS: proteome-wide association study—linking genes and phenotypes by functional variation in proteins
por: Brandes, Nadav, et al.
Publicado: (2020)

A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness
por: Katsonis, Panagiotis, et al.
Publicado: (2014)

Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets
por: Jourdain, Jeanlin, et al.
Publicado: (2023)

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq
por: Buettner, Florian, et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_ak0hdhvatsc8clr6mkd6s7l45a