Cargando…

FastBMD: an online tool for rapid benchmark dose–response analysis of transcriptomics data

MOTIVATION: Transcriptomics dose–response analysis is a promising new approach method for toxicity testing. While international regulatory agencies have spent substantial effort establishing a standardized statistical approach, existing software that follows this approach is computationally ineffici...

Descripción completa

Detalles Bibliográficos
Autores principales:	Ewald, Jessica, Soufan, Othman, Xia, Jianguo, Basu, Niladri
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2020
Materias:	Applications Notes
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8128449/ https://www.ncbi.nlm.nih.gov/pubmed/32761065 http://dx.doi.org/10.1093/bioinformatics/btaa700

Ejemplares similares

bmd: an R package for benchmark dose estimation
por: Jensen, Signe M., et al.
Publicado: (2020)

BBKNN: fast batch alignment of single cell transcriptomes
por: Polański, Krzysztof, et al.
Publicado: (2019)

FastSpar: rapid and scalable correlation estimation for compositional data
por: Watts, Stephen C, et al.
Publicado: (2019)

WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools
por: Rackham, Owen J. L., et al.
Publicado: (2015)

benchdamic: benchmarking of differential abundance methods for microbiome data
por: Calgaro, Matteo, et al.
Publicado: (2022)

NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis
por: Zhou, Guangyan, et al.
Publicado: (2019)

T1000: a reduced gene set prioritized for toxicogenomic studies
por: Soufan, Othman, et al.
Publicado: (2019)

Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python
por: Lubbock, Alexander L R, et al.
Publicado: (2022)

Canto: an online tool for community literature curation
por: Rutherford, Kim M., et al.
Publicado: (2014)

orfipy: a fast and flexible tool for extracting ORFs
por: Singh, Urminder, et al.
Publicado: (2021)

Pharokka: a fast scalable bacteriophage annotation tool
por: Bouras, George, et al.
Publicado: (2022)

genozip: a fast and efficient compression tool for VCF files
por: Lan, Divon, et al.
Publicado: (2020)

MAGScoT: a fast, lightweight and accurate bin-refinement tool
por: Rühlemann, Malte Christoph, et al.
Publicado: (2022)

immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking
por: Weber, Cédric R, et al.
Publicado: (2020)

PMLB v1.0: an open-source dataset collection for benchmarking machine learning methods
por: Romano, Joseph D, et al.
Publicado: (2021)

GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations
por: Dickson, Andrew, et al.
Publicado: (2023)

Enabling a fast annotation process with the Table2Annotation tool
por: Larmande, Pierre, et al.
Publicado: (2020)

nestedcv: an R package for fast implementation of nested cross-validation with embedded feature selection designed for transcriptomics and high-dimensional data
por: Lewis, Myles J, et al.
Publicado: (2023)

CycSim—an online tool for exploring and experimenting with genome-scale metabolic models
por: Le Fèvre, F., et al.
Publicado: (2009)

The ENDS of assumptions: an online tool for the epistemic non-parametric drug–response scoring
por: Amiryousefi, Ali, et al.
Publicado: (2022)

pyconsFold: a fast and easy tool for modeling and docking using distance predictions
por: Lamb, J, et al.
Publicado: (2021)

Cas-analyzer: an online tool for assessing genome editing results using NGS data
por: Park, Jeongbin, et al.
Publicado: (2017)

EFMDR-Fast: An Application of Empirical Fuzzy Multifactor Dimensionality Reduction for Fast Execution
por: Leem, Sangseob, et al.
Publicado: (2018)

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix
por: Ambrosini, Giovanna, et al.
Publicado: (2018)

Viral Host Range database, an online tool for recording, analyzing and disseminating virus–host interactions
por: Lamy-Besnier, Quentin, et al.
Publicado: (2021)

Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud
por: Di Tommaso, Paolo, et al.
Publicado: (2010)

ProteoWizard: open source software for rapid proteomics tools development
por: Kessner, Darren, et al.
Publicado: (2008)

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
por: Kozlov, Alexey M, et al.
Publicado: (2019)

MELODI Presto: a fast and agile tool to explore semantic triples derived from biomedical literature
por: Elsworth, Benjamin, et al.
Publicado: (2020)

HiCLift: a fast and efficient tool for converting chromatin interaction data between genome assemblies
por: Wang, Xiaotao, et al.
Publicado: (2023)

Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data
por: García-Alcalde, Fernando, et al.
Publicado: (2011)

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
por: Zhao, Yongan, et al.
Publicado: (2012)

siMacro: A Fast and Easy Data Processing Tool for Cell-Based Genomewide siRNA Screens
por: Singh, Nitin Kumar, et al.
Publicado: (2013)

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters
por: Chu, Justin, et al.
Publicado: (2014)

DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis
por: Aureli, Simone, et al.
Publicado: (2019)

FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool
por: Brown, Joseph, et al.
Publicado: (2017)

FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution
por: Li, Mulin Jun, et al.
Publicado: (2010)

Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes
por: Cleemput, Sara, et al.
Publicado: (2020)

Sambamba: fast processing of NGS alignment formats
por: Tarasov, Artem, et al.
Publicado: (2015)

Fast and sensitive taxonomic assignment to metagenomic contigs
por: Mirdita, M, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_is994jgp1jga6umhodmbu35536