Cargando…

BGData - A Suite of R Packages for Genomic Analysis with Big Data

We created a suite of packages to enable analysis of extremely large genomic data sets (potentially millions of individuals and millions of molecular markers) within the R environment. The package offers: a matrix-like interface for .bed files (PLINK’s binary format for genotype data), a novel class...

Descripción completa

Detalles Bibliográficos
Autores principales:	Grueneberg, Alexander, de los Campos, Gustavo
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Genetics Society of America 2019
Materias:	Software and Data Resources
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6505159/ https://www.ncbi.nlm.nih.gov/pubmed/30894453 http://dx.doi.org/10.1534/g3.119.400018

Ejemplares similares

Interactively AUDIT Your Growth Curves with a Suite of R Packages
por: Coutin, Nicolas P. J., et al.
Publicado: (2020)

GWLD: an R package for genome-wide linkage disequilibrium analysis
por: Zhang, Rong, et al.
Publicado: (2023)

An R Package for Bayesian Analysis of Multi-environment and Multi-trait Multi-environment Data for Genome-Based Prediction
por: Montesinos-López, Osval A., et al.
Publicado: (2019)

rSalvador: An R Package for the Fluctuation Experiment
por: Zheng, Qi
Publicado: (2017)

learnMET: an R package to apply machine learning methods for genomic prediction using multi-environment trial data
por: Westhues, Cathy C, et al.
Publicado: (2022)

CaveCrawler: an interactive analysis suite for cavefish bioinformatics
por: Perry, Annabel, et al.
Publicado: (2022)

AlphaSimR: an R package for breeding program simulations
por: Gaynor, R Chris, et al.
Publicado: (2020)

gJLS2: an R package for generalized joint location and scale analysis in X-inclusive genome-wide association studies
por: Deng, Wei Q, et al.
Publicado: (2022)

vqtl: An R Package for Mean-Variance QTL Mapping
por: Corty, Robert W., et al.
Publicado: (2018)

Ghat: an R package for identifying adaptive polygenic traits
por: Mahmoud, Medhat, et al.
Publicado: (2022)

stuart: an R package for the curation of SNP genotypes from experimental crosses
por: Bourdon, Marie, et al.
Publicado: (2022)

OCMA: Fast, Memory-Efficient Factorization of Prohibitively Large Relationship Matrices
por: Xiong, Zhi, et al.
Publicado: (2018)

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data
por: Kishore, Kamal, et al.
Publicado: (2015)

rdmc: An Open Source R Package Implementing Convergent Adaptation Models of Lee and Coop (2017)
por: Tittes, Silas
Publicado: (2020)

GWideCodeML: A Python Package for Testing Evolutionary Hypotheses at the Genome-Wide Level
por: Macías, Laura G., et al.
Publicado: (2020)

CDMAP/CDVIS: context-dependent mutation analysis package and visualization software
por: Patton, David L, et al.
Publicado: (2022)

genomicSimulation: fast R functions for stochastic simulation of breeding programs
por: Villiers, Kira, et al.
Publicado: (2022)

Will Big Data Close the Missing Heritability Gap?
por: Kim, Hwasoon, et al.
Publicado: (2017)

Mass-Suite: a novel open-source python package for high-resolution mass spectrometry data analysis
por: Hu, Ximin, et al.
Publicado: (2023)

Whole Animal Genome Sequencing: user-friendly, rapid, containerized pipelines for processing, variant discovery, and annotation of short-read whole genome sequencing data
por: Cullen, Jonah N, et al.
Publicado: (2023)

plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style
por: Cao, Tianze, et al.
Publicado: (2023)

GCA: an R package for genetic connectedness analysis using pedigree and genomic data
por: Yu, Haipeng, et al.
Publicado: (2021)

GENLIB: an R package for the analysis of genealogical data
por: Gauvin, Héloïse, et al.
Publicado: (2015)

ggbio: an R package for extending the grammar of graphics for genomic data
por: Yin, Tengfei, et al.
Publicado: (2012)

polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids
por: Clark, Lindsay V., et al.
Publicado: (2019)

Model Organism Modifier (MOM): a user-friendly Galaxy workflow to detect modifiers from genome sequencing data using Caenorhabditis elegans
por: Maroilley, Tatiana, et al.
Publicado: (2023)

SECIMTools: a suite of metabolomics data analysis tools
por: Kirpich, Alexander S., et al.
Publicado: (2018)

Next-generation sequencing-based bulked segregant analysis without sequencing the parental genomes
por: Zhang, Jianbo, et al.
Publicado: (2021)

ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data
por: Orjuela, Stephany, et al.
Publicado: (2019)

A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication
por: De-Kayne, Rishi, et al.
Publicado: (2018)

MetaPrism: A versatile toolkit for joint taxa/gene analysis of metagenomic sequencing data
por: Kim, Jiwoong, et al.
Publicado: (2021)

GEDAS ‐ Gene Expression Data Analysis Suite
por: Prasad, Tangirala Venkateswara, et al.
Publicado: (2006)

BLAST-XYPlot Viewer: A Tool for Performing BLAST in Whole-Genome Sequenced Bacteria/Archaea and Visualize Whole Results Simultaneously
por: Pedraza-Pérez, Yagul, et al.
Publicado: (2018)

AMDA: an R package for the automated microarray data analysis
por: Pelizzola, Mattia, et al.
Publicado: (2006)

renz: An R package for the analysis of enzyme kinetic data
por: Aledo, Juan Carlos
Publicado: (2022)

FrAnTK: a Frequency-based Analysis ToolKit for efficient exploration of allele sharing patterns in present-day and ancient genomic datasets
por: Moreno-Mayar, J Víctor
Publicado: (2021)

Matrisome AnalyzeR – a suite of tools to annotate and quantify ECM molecules in big datasets across organisms
por: Petrov, Petar B., et al.
Publicado: (2023)

micRocounter: Microsatellite Characterization in Genome Assemblies
por: Lo, Johnathan, et al.
Publicado: (2019)

Eagle for better genome-wide association mapping
por: George, Andrew W, et al.
Publicado: (2021)

EXPANDER – an integrative program suite for microarray data analysis
por: Shamir, Ron, et al.
Publicado: (2005)

Cannot write session to /tmp/vufind_sessions/sess_5823foutj85v0huvl5v2ijnr65