Cargando…

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

ZINBA (Zero-Inflated Negative Binomial Algorithm) identifies genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes of enrichment across a range of signal-to-noise ratios. ZINBA models and accounts for facto...

Descripción completa

Detalles Bibliográficos
Autores principales:	Rashid, Naim U, Giresi, Paul G, Ibrahim, Joseph G, Sun, Wei, Lieb, Jason D
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2011
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218829/ https://www.ncbi.nlm.nih.gov/pubmed/21787385 http://dx.doi.org/10.1186/gb-2011-12-7-r67

Ejemplares similares

MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework
por: Harmanci, Arif, et al.
Publicado: (2014)

STARRPeaker: uniform processing and accurate identification of STARR-seq active regions
por: Lee, Donghoon, et al.
Publicado: (2020)

ATAC-STARR-seq reveals transcription factor–bound activators and silencers within chromatin-accessible regions of the human genome
por: Hansen, Tyler J., et al.
Publicado: (2022)

Identification of pathogenic variant enriched regions across genes and gene families
por: Pérez-Palma, Eduardo, et al.
Publicado: (2020)

Broad-Enrich: functional interpretation of large sets of broad genomic regions
por: Cavalcante, Raymond G., et al.
Publicado: (2014)

Flexible expressed region analysis for RNA-seq with derfinder
por: Collado-Torres, Leonardo, et al.
Publicado: (2017)

Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing
por: Kawaji, Hideya, et al.
Publicado: (2014)

ChIP-Enrich: gene set enrichment testing for ChIP-seq data
por: Welch, Ryan P., et al.
Publicado: (2014)

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

Covariation Is a Poor Measure of Molecular Coevolution
por: Talavera, David, et al.
Publicado: (2015)

COCOA: coordinate covariation analysis of epigenetic heterogeneity
por: Lawson, John T., et al.
Publicado: (2020)

Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment
por: Yan, Bo, et al.
Publicado: (2022)

Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes
por: Lu, Zefu, et al.
Publicado: (2017)

High-resolution nucleosome mapping of targeted regions using BAC-based enrichment
por: Yigit, Erbay, et al.
Publicado: (2013)

Sensitive and inexpensive digital DNA analysis by microfluidic enrichment of rolling circle amplified single-molecules
por: Kühnemund, Malte, et al.
Publicado: (2017)

Selecting Optimal Subgroups for Treatment Using Many Covariates
por: VanderWeele, Tyler J., et al.
Publicado: (2019)

Fast analysis of scATAC-seq data using a predefined set of genomic regions
por: Giansanti, Valentina, et al.
Publicado: (2020)

Commentary: An Even Clearer Portrait of Bias in Observational Studies?
por: Davies, Neil M.
Publicado: (2015)

Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains
por: Starmer, Joshua, et al.
Publicado: (2016)

Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions
por: De Preter, Katleen, et al.
Publicado: (2008)

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

STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer
por: Fleming, Joseph D, et al.
Publicado: (2015)

Nanoelectromechanical resonant narrow-band amplifiers
por: Ramezany, Alireza, et al.
Publicado: (2016)

Targeted genome fragmentation with CRISPR/Cas9 enables fast and efficient enrichment of small genomic regions and ultra-accurate sequencing with low DNA input (CRISPR-DS)
por: Nachmanson, Daniela, et al.
Publicado: (2018)

An NMF-based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq data
por: Matsumoto, Hirotaka, et al.
Publicado: (2019)

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions
por: Schep, Alicia N., et al.
Publicado: (2015)

Search for narrow resonances in the R region
por: Bowen, D, et al.
Publicado: (1972)

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

Bias in two-sample Mendelian randomization when using heritable covariable-adjusted summary associations
por: Hartwig, Fernando Pires, et al.
Publicado: (2021)

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)

Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery
por: Aggeli, Dimitra, et al.
Publicado: (2018)

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)

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly
por: Lun, Aaron T.L., et al.
Publicado: (2014)

Identification of transcription factor binding sites using ATAC-seq
por: Li, Zhijian, et al.
Publicado: (2019)

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

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells
por: Fuchs, Gilad, et al.
Publicado: (2014)

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)

Cannot write session to /tmp/vufind_sessions/sess_1snlmnnhba4lefk40nr2on3ip0