Cargando…

The Tomato Expression Atlas

SUMMARY: With the development of new high-throughput DNA sequencing technologies and decreasing costs, large gene expression datasets are being generated at an accelerating rate, but can be complex to visualize. New, more interactive and intuitive tools are needed to visualize the spatiotemporal con...

Descripción completa

Detalles Bibliográficos
Autores principales:	Fernandez-Pozo, Noe, Zheng, Yi, Snyder, Stephen I, Nicolas, Philippe, Shinozaki, Yoshihito, Fei, Zhangjun, Catala, Carmen, Giovannoni, James J, Rose, Jocelyn K.C, Mueller, Lukas A
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2017
Materias:	Applications Notes
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860121/ https://www.ncbi.nlm.nih.gov/pubmed/28379331 http://dx.doi.org/10.1093/bioinformatics/btx190

Ejemplares similares

High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening
por: Shinozaki, Yoshihito, et al.
Publicado: (2018)

EasyGDB: a low-maintenance and highly customizable system to develop genomics portals
por: Fernandez-Pozo, Noe, et al.
Publicado: (2022)

Porechop_ABI: discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming
por: Bonenfant, Quentin, et al.
Publicado: (2022)

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries
por: Habegger, Lukas, et al.
Publicado: (2011)

The tomato HIGH PIGMENT1/DAMAGED DNA BINDING PROTEIN 1 gene contributes to regulation of fruit ripening
por: Wang, Anquan, et al.
Publicado: (2019)

Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding
por: Wang, Xin, et al.
Publicado: (2020)

Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information
por: Tong, Joo Chuan, et al.
Publicado: (2009)

FoldAtlas: a repository for genome-wide RNA structure probing data
por: Norris, Matthew, et al.
Publicado: (2017)

AtlasXplore: a web platform for visualizing and sharing spatial epigenome data
por: Barnett, Joshua, et al.
Publicado: (2023)

RCSB Protein Data Bank 1D tools and services
por: Segura, Joan, et al.
Publicado: (2020)

RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies
por: Segura, Joan, et al.
Publicado: (2022)

Tomato Expression Database (TED): a suite of data presentation and analysis tools
por: Fei, Zhangjun, et al.
Publicado: (2006)

sBGC-hm: an atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome
por: Zou, Huixi, et al.
Publicado: (2023)

Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank
por: Prlić, Andreas, et al.
Publicado: (2016)

RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB
por: Bittrich, Sebastian, et al.
Publicado: (2021)

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
por: Phanstiel, Douglas H., et al.
Publicado: (2014)

PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data
por: Nair, Sreenath, et al.
Publicado: (2021)

netReg: network-regularized linear models for biological association studies
por: Dirmeier, Simon, et al.
Publicado: (2018)

metID: an R package for automatable compound annotation for LC−MS-based data
por: Shen, Xiaotao, et al.
Publicado: (2021)

JEasyTFM: an open-source software package for the analysis of large 2D TFM data within ImageJ
por: Carl, Philippe, et al.
Publicado: (2023)

Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package
por: Rodrigue, Nicolas, et al.
Publicado: (2014)

qvality: non-parametric estimation of q-values and posterior error probabilities
por: Käll, Lukas, et al.
Publicado: (2009)

WAVES (Web-based tool for Analysis and Visualization of Environmental Samples)—a web application for visualization of wastewater pathogen sequencing results
por: Triska, Petr, et al.
Publicado: (2023)

HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens
por: Wang, Xin, et al.
Publicado: (2011)

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments
por: Lienhard, Matthias, et al.
Publicado: (2014)

ELIXIR biovalidator for semantic validation of life science metadata
por: Liyanage, Isuru, et al.
Publicado: (2022)

Finding enzyme cofactors in Protein Data Bank
por: Mukhopadhyay, Abhik, et al.
Publicado: (2019)

monaLisa: an R/Bioconductor package for identifying regulatory motifs
por: Machlab, Dania, et al.
Publicado: (2022)

CANDI: an R package and Shiny app for annotating radiographs and evaluating computer-aided diagnosis
por: Badgeley, Marcus A, et al.
Publicado: (2019)

OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts
por: Ravagli, Carlo, et al.
Publicado: (2017)

JSBML: a flexible Java library for working with SBML
por: Dräger, Andreas, et al.
Publicado: (2011)

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level
por: Rocca-Serra, Philippe, et al.
Publicado: (2010)

NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data
por: Waggott, Daryl, et al.
Publicado: (2012)

LASER server: ancestry tracing with genotypes or sequence reads
por: Taliun, Daniel, et al.
Publicado: (2017)

Transgenic strategies to generate heterogeneous hepatic cancer models in zebrafish
por: Fei, Fei, et al.
Publicado: (2019)

MiSDEED: a synthetic data engine for microbiome study power analysis and study design
por: Chlenski, Philippe, et al.
Publicado: (2022)

NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID
por: Gaudreault, Francis, et al.
Publicado: (2015)

Pre-calculated protein structure alignments at the RCSB PDB website
por: Prlić, Andreas, et al.
Publicado: (2010)

HiCBricks: building blocks for efficient handling of large Hi-C datasets
por: Pal, Koustav, et al.
Publicado: (2020)

cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data
por: Eling, Nils, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_o03rt03l9picacetggjkdjp373