Cargando…

RADAR: differential analysis of MeRIP-seq data with a random effect model

Epitranscriptome profiling using MeRIP-seq is a powerful technique for in vivo functional studies of reversible RNA modifications. We develop RADAR, a comprehensive analytical tool for detecting differentially methylated loci in MeRIP-seq data. RADAR enables accurate identification of altered methyl...

Descripción completa

Detalles Bibliográficos
Autores principales:	Zhang, Zijie, Zhan, Qi, Eckert, Mark, Zhu, Allen, Chryplewicz, Agnieszka, De Jesus, Dario F., Ren, Decheng, Kulkarni, Rohit N., Lengyel, Ernst, He, Chuan, Chen, Mengjie
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2019
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6927177/ https://www.ncbi.nlm.nih.gov/pubmed/31870409 http://dx.doi.org/10.1186/s13059-019-1915-9

Ejemplares similares

MeRIP-PF: An Easy-to-use Pipeline for High-resolution Peak-finding in MeRIP-Seq Data
por: Li, Yuli, et al.
Publicado: (2013)

MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq
por: Zhang, Yiqian, et al.
Publicado: (2020)

A hierarchical model for clustering m(6)A methylation peaks in MeRIP-seq data
por: Cui, Xiaodong, et al.
Publicado: (2016)

Limits in the detection of m(6)A changes using MeRIP/m(6)A-seq
por: McIntyre, Alexa B. R., et al.
Publicado: (2020)

Identification and comparison of m6A modifications in glioblastoma non-coding RNAs with MeRIP-seq and Nanopore dRNA-seq
por: Krusnauskas, Raulas, et al.
Publicado: (2023)

Comprehensive Analysis of the Transcriptome-Wide m6A Methylome in Pterygium by MeRIP Sequencing
por: Jiang, Yaping, et al.
Publicado: (2021)

A novel algorithm for calling mRNA m(6)A peaks by modeling biological variances in MeRIP-seq data
por: Cui, Xiaodong, et al.
Publicado: (2016)

Validated Impacts of N6-Methyladenosine Methylated mRNAs on Apoptosis and Angiogenesis in Myocardial Infarction Based on MeRIP-Seq Analysis
por: Zhang, Yingjie, et al.
Publicado: (2022)

Comprehensive analysis of m(6)A circRNAs identified in colorectal cancer by MeRIP sequencing
por: He, Feng, et al.
Publicado: (2022)

Comprehensive Analysis of the Transcriptome-wide m6A Methylome in Lung Adenocarcinoma by MeRIP Sequencing
por: Mao, Wenli, et al.
Publicado: (2022)

Corrigendum: Comprehensive analysis of the transcriptome-wide m6A methylome in lung adenocarcinoma by MeRIP sequencing
por: Mao, Wenli, et al.
Publicado: (2022)

Comprehensive Analysis of 5-Methylcytosine Profiles of Messenger RNA in Human High-Grade Serous Ovarian Cancer by MeRIP Sequencing
por: Meng, Li, et al.
Publicado: (2021)

The Important Role of m6A-Modified circRNAs in the Differentiation of Intramuscular Adipocytes in Goats Based on MeRIP Sequencing Analysis
por: Wang, Jianmei, et al.
Publicado: (2023)

Mapping the m1A, m5C, m6A and m7G methylation atlas in zebrafish brain under hypoxic conditions by MeRIP-seq
por: Li, Wei, et al.
Publicado: (2022)

Comprehensive Analysis of the Transcriptome-Wide m6A Methylome of Heart via MeRIP After Birth: Day 0 vs. Day 7
por: Yang, Chuanxi, et al.
Publicado: (2021)

Identifying key m(6)A-methylated lncRNAs and genes associated with neural tube defects via integrative MeRIP and RNA sequencing analyses
por: Yang, Jing, et al.
Publicado: (2022)

Refined RIP-seq protocol for epitranscriptome analysis with low input materials
por: Zeng, Yong, et al.
Publicado: (2018)

Corrigendum: Identifying key m(6)A-methylated lncRNAs and genes associated with neural tube defects via integrative MeRIP and RNA sequencing analyses
por: Yang, Jing, et al.
Publicado: (2023)

RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments
por: Li, Yue, et al.
Publicado: (2013)

Mutant p53 regulates LPA signaling through lysophosphatidic acid phosphatase type 6
por: Chryplewicz, Agnieszka, et al.
Publicado: (2019)

Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching
por: Chen, Mengjie, et al.
Publicado: (2021)

Illumina-based RiboMethSeq approach for mapping of 2′-O-Me residues in RNA
por: Marchand, Virginie, et al.
Publicado: (2016)

SeqOthello: querying RNA-seq experiments at scale
por: Yu, Ye, et al.
Publicado: (2018)

A benchmark for RNA-seq quantification pipelines
por: Teng, Mingxiang, et al.
Publicado: (2016)

Comparison of iSeq and MiSeq as the two platforms for 16S rRNA sequencing in the study of the gut of rat microbiome
por: Salamon, Dominika, et al.
Publicado: (2022)

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

Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency
por: Adamson, Scott I., et al.
Publicado: (2018)

CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins
por: Savic, Daniel, et al.
Publicado: (2015)

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

Correcting signal biases and detecting regulatory elements in STARR-seq data
por: Kim, Young-Sook, et al.
Publicado: (2021)

Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq
por: Liu, Peng, et al.
Publicado: (2016)

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

RIP-chip-SRM—a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans
por: Jovanovic, Marko, et al.
Publicado: (2012)

The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing
por: Cieslik, Marcin, et al.
Publicado: (2015)

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome
por: Howald, Cédric, et al.
Publicado: (2012)

EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation
por: Lhoumaud, Priscillia, et al.
Publicado: (2019)

HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples
por: Chen, Haojie, et al.
Publicado: (2022)

A deep generative model for multi-view profiling of single-cell RNA-seq and ATAC-seq data
por: Li, Gaoyang, et al.
Publicado: (2022)

Identification of the miRNA targetome in hippocampal neurons using RIP-seq
por: Malmevik, Josephine, et al.
Publicado: (2015)

RIP-Seq Suggests Translational Regulation by L7Ae in Archaea
por: Daume, Michael, et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_n7f5os4vqs8945ao6vqhnkqh0c