Cargando…

RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data

BACKGROUND: Ribo-seq is a popular technique for studying translation and its regulation. A Ribo-seq experiment produces a snap-shot of the location and abundance of actively translating ribosomes within a cell’s transcriptome. In practice, Ribo-seq data analysis can be sensitive to quality issues su...

Descripción completa

Detalles Bibliográficos
Autores principales:	Perkins, Patrick, Mazzoni-Putman, Serina, Stepanova, Anna, Alonso, Jose, Heber, Steffen
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2019
Materias:	Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6551240/ https://www.ncbi.nlm.nih.gov/pubmed/31167636 http://dx.doi.org/10.1186/s12864-019-5700-7

Ejemplares similares

RiboPlotR: a visualization tool for periodic Ribo-seq reads
por: Wu, Hsin-Yen Larry, et al.
Publicado: (2021)

Ribo-ODDR: oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq
por: Alkan, Ferhat, et al.
Publicado: (2021)

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

RiboFlow, RiboR and RiboPy: an ecosystem for analyzing ribosome profiling data at read length resolution
por: Ozadam, Hakan, et al.
Publicado: (2020)

RiboDiPA: a novel tool for differential pattern analysis in Ribo-seq data
por: Li, Keren, et al.
Publicado: (2020)

Ribo-seq enlightens codon usage bias
por: Paulet, Damien, et al.
Publicado: (2017)

Structured RNA Contaminants in Bacterial Ribo-Seq
por: Fremin, Brayon J., et al.
Publicado: (2020)

MetaRibo-Seq measures translation in microbiomes
por: Fremin, Brayon J., et al.
Publicado: (2020)

sncRiboTag-Seq: cell-type-specific RiboTag-Seq for cells in low abundance in mouse brain tissue
por: Gao, Yu, et al.
Publicado: (2020)

A tool for analyzing and visualizing ribo-seq data at the isoform level
por: Wu, Wei-Sheng, et al.
Publicado: (2021)

High-throughput translational profiling with riboPLATE-seq
por: Metz, Jordan B., et al.
Publicado: (2022)

GWIPS-viz: development of a ribo-seq genome browser
por: Michel, Audrey M., et al.
Publicado: (2014)

Improved Ribo-seq enables identification of cryptic translation events
por: Erhard, Florian, et al.
Publicado: (2018)

STATR: A simple analysis pipeline of Ribo-Seq in bacteria
por: Choe, Donghui, et al.
Publicado: (2020)

Trips-Viz: a transcriptome browser for exploring Ribo-Seq data
por: Kiniry, Stephen J, et al.
Publicado: (2019)

The potential of the riboSNitch in personalized medicine
por: Solem, Amanda C., et al.
Publicado: (2015)

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq
por: Aspden, Julie L, et al.
Publicado: (2014)

Prebiotic Photochemical Coproduction of Purine Ribo- and Deoxyribonucleosides
por: Xu, Jianfeng, et al.
Publicado: (2021)

RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes
por: Zhang, Yanming, et al.
Publicado: (2016)

RiboXYZ: a comprehensive database for visualizing and analyzing ribosome structures
por: Kushner, Artem, et al.
Publicado: (2022)

Ribo-On and Ribo-Off tools using a self-cleaving ribozyme allow manipulation of endogenous gene expression in C. elegans
por: Fang, Jie, et al.
Publicado: (2023)

DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data
por: Cui, Hongfei, et al.
Publicado: (2019)

What can Ribo-seq and proteomics tell us about the non-canonical proteome?
por: Prensner, John R., et al.
Publicado: (2023)

What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?
por: Prensner, John R., et al.
Publicado: (2023)

deltaTE: Detection of Translationally Regulated Genes by Integrative Analysis of Ribo‐seq and RNA‐seq Data
por: Chothani, Sonia, et al.
Publicado: (2019)

Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture
por: Mahboubi, Amir, et al.
Publicado: (2021)

RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes
por: Lucier, Jean-François, et al.
Publicado: (2006)

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

Optimization of Ribosome Footprinting Conditions for Ribo-Seq in Human and Drosophila melanogaster Tissue Culture Cells
por: Douka, Katerina, et al.
Publicado: (2022)

Tracing Translational Footprint by Ribo-Seq: Principle, Workflow, and Applications to Understand the Mechanism of Human Diseases
por: Bagheri, Atefeh, et al.
Publicado: (2022)

RiboVIEW: a computational framework for visualization, quality control and statistical analysis of ribosome profiling data
por: Legrand, Carine, et al.
Publicado: (2020)

RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data
por: Michel, Audrey M., et al.
Publicado: (2016)

Ribo-Seq and RNA-Seq of TMA46 (DFRP1) and GIR2 (DFRP2) knockout yeast strains
por: Egorov, Artyom A., et al.
Publicado: (2021)

High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq
por: Gumienny, Rafal, et al.
Publicado: (2017)

RNA-Seq of human whole blood: Evaluation of globin RNA depletion on Ribo-Zero library method
por: Harrington, Christina A., et al.
Publicado: (2020)

Transcriptomic Profiling of Zebrafish Hair Cells Using RiboTag
por: Matern, Maggie S., et al.
Publicado: (2018)

The genetic insulator RiboJ increases expression of insulated genes
por: Clifton, Kalen P., et al.
Publicado: (2018)

Ribo-attenuators: novel elements for reliable and modular riboswitch engineering
por: Folliard, Thomas, et al.
Publicado: (2017)

Visualisation of ribosomes in Drosophila axons using Ribo-BiFC
por: Singh, Anand K., et al.
Publicado: (2020)

riboCIRC: a comprehensive database of translatable circRNAs
por: Li, Huihui, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_fhvg9vb8a7v46ov4os7rer9org