Cargando…

Viewing RNA-seq data on the entire human genome

RNA-Seq Viewer is a web application that enables users to visualize genome-wide expression data from NCBI’s Sequence Read Archive (SRA) and Gene Expression Omnibus (GEO) databases. The application prototype was created by a small team during a three-day hackathon facilitated by NCBI at Brandeis Univ...

Descripción completa

Detalles Bibliográficos
Autores principales:	Weitz, Eric M., Pantano, Lorena, Zhu, Jingzhi, Upton, Bennett, Busby, Ben
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	F1000Research 2017
Materias:	Software Tool Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5605993/ https://www.ncbi.nlm.nih.gov/pubmed/28979763 http://dx.doi.org/10.12688/f1000research.9762.1

Ejemplares similares

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis
por: Ather, Syed Hussain, et al.
Publicado: (2020)

Visualization of the small RNA transcriptome using seqclusterViz
por: Pantano, Lorena, et al.
Publicado: (2019)

RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting
por: Jensen, Travis L., et al.
Publicado: (2018)

Extending TCGA queries to automatically identify analogous genomic data from dbGaP
por: Wagner, Erin K., et al.
Publicado: (2017)

SeqPlots - Interactive software for exploratory data analyses, pattern discovery and visualization in genomics
por: Stempor, Przemyslaw, et al.
Publicado: (2016)

MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis
por: Moyer, Eric, et al.
Publicado: (2016)

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
por: Lun, Aaron T.L., et al.
Publicado: (2016)

Making the most of RNA-seq: Pre-processing sequencing data with Opossum for reliable SNP variant detection
por: Oikkonen, Laura, et al.
Publicado: (2017)

NovoGraph: Human genome graph construction from multiple long-read de novo assemblies
por: Biederstedt, Evan, et al.
Publicado: (2018)

Magic-BLAST, an accurate RNA-seq aligner for long and short reads
por: Boratyn, Grzegorz M., et al.
Publicado: (2019)

DangerTrack: A scoring system to detect difficult-to-assess regions
por: Dolgalev, Igor, et al.
Publicado: (2017)

dbVar structural variant cluster set for data analysis and variant comparison
por: Phan, Lon, et al.
Publicado: (2017)

RNfuzzyApp: an R shiny RNA-seq data analysis app for visualisation, differential expression analysis, time-series clustering and enrichment analysis
por: Haering, Margaux, et al.
Publicado: (2021)

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
por: Law, Charity W., et al.
Publicado: (2018)

ReactomeFIViz: a Cytoscape app for pathway and network-based data analysis
por: Wu, Guanming, et al.
Publicado: (2014)

From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data
por: Lun, Aaron T. L., et al.
Publicado: (2016)

edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens
por: Dai, Zhiyin, et al.
Publicado: (2014)

CoverView: a sequence quality evaluation tool for next generation sequencing data
por: Münz, Márton, et al.
Publicado: (2018)

PubRunner: A light-weight framework for updating text mining results
por: Anekalla, Kishore R., et al.
Publicado: (2017)

Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive
por: Bernstein, Matthew N., et al.
Publicado: (2020)

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
por: Chen, Yunshun, et al.
Publicado: (2016)

Cytoscape: the network visualization tool for GenomeSpace workflows
por: Demchak, Barry, et al.
Publicado: (2014)

KEGGscape: a Cytoscape app for pathway data integration
por: Nishida, Kozo, et al.
Publicado: (2014)

EpiCollect+: linking smartphones to web applications for complex data collection projects
por: Aanensen, David M., et al.
Publicado: (2014)

Expresso: A database and web server for exploring the interaction of transcription factors and their target genes in Arabidopsis thaliana using ChIP-Seq peak data
por: Aghamirzaie, Delasa, et al.
Publicado: (2017)

RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing
por: Popa, Alexandra, et al.
Publicado: (2016)

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
por: Li, Bo, et al.
Publicado: (2011)

Cascade: an RNA-seq visualization tool for cancer genomics
por: Shifman, Aaron R., et al.
Publicado: (2016)

Transcript mapping based on dRNA-seq data
por: Bischler, Thorsten, et al.
Publicado: (2014)

EPIG-Seq: extracting patterns and identifying co-expressed genes from RNA-Seq data
por: Li, Jianying, et al.
Publicado: (2016)

intePareto: an R package for integrative analyses of RNA-Seq and ChIP-Seq data
por: Cao, Yingying, et al.
Publicado: (2020)

ClinVar data parsing
por: Zhang, Xiaolei, et al.
Publicado: (2017)

FRAMA: from RNA-seq data to annotated mRNA assemblies
por: Bens, Martin, et al.
Publicado: (2016)

TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data
por: Chiu, Readman, et al.
Publicado: (2018)

lmerSeq: an R package for analyzing transformed RNA-Seq data with linear mixed effects models
por: Vestal, Brian E., et al.
Publicado: (2022)

Kvik: three-tier data exploration tools for flexible analysis of genomic data in epidemiological studies
por: Fjukstad, Bjørn, et al.
Publicado: (2015)

TSSAR: TSS annotation regime for dRNA-seq data
por: Amman, Fabian, et al.
Publicado: (2014)

T-REx: Transcriptome analysis webserver for RNA-seq Expression data
por: de Jong, Anne, et al.
Publicado: (2015)

FastqPuri: high-performance preprocessing of RNA-seq data
por: Pérez-Rubio, Paula, et al.
Publicado: (2019)

Negative binomial additive model for RNA-Seq data analysis
por: Ren, Xu, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_ve5b797duoovefv24ul15rl2vo