Cargando…

An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays

Illumina Infinium DNA methylation arrays are a cost-effective technology to measure DNA methylation at CpG sites genome-wide and across cohorts of normal and cancer samples. While copy number alterations are commonly inferred from array-CGH, SNP arrays, or whole-genome DNA sequencing, Illumina Infin...

Descripción completa

Detalles Bibliográficos
Autores principales:	Mah, Clarence K., Mesirov, Jill P., Chavez, Lukas
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	F1000 Research Limited 2018
Materias:	Software Tool Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6498745/ https://www.ncbi.nlm.nih.gov/pubmed/31105932 http://dx.doi.org/10.12688/f1000research.16338.1

Ejemplares similares

An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data
por: Mah, Clarence K., et al.
Publicado: (2019)

shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R
por: Fortin, Jean-Philippe, et al.
Publicado: (2014)

CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations
por: Kotliarov, Yuri, et al.
Publicado: (2010)

Low-level processing of Illumina Infinium DNA Methylation BeadArrays
por: Triche, Timothy J., et al.
Publicado: (2013)

GenePattern flow cytometry suite
por: Spidlen, Josef, et al.
Publicado: (2013)

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

Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios
por: Staaf, Johan, et al.
Publicado: (2008)

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

Evaluation of copy number variation detection for a SNP array platform
por: Zhang, Xin, et al.
Publicado: (2014)

An Approach to Improve Laboratory Notebook Feedback and Decrease Instructor Fatigue from Grading Undergraduate Laboratory Notebooks
por: Fleming, Emily J.
Publicado: (2023)

Constellation Map: Downstream visualization and interpretation of gene set enrichment results
por: Tan, Yan, et al.
Publicado: (2015)

GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes
por: van den Broek, Evert, et al.
Publicado: (2017)

SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips
por: Maksimovic, Jovana, et al.
Publicado: (2012)

Infinium Monkeys: Infinium 450K Array for the Cynomolgus macaque (Macaca fascicularis)
por: Ong, Mei-Lyn, et al.
Publicado: (2014)

InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor
por: Coletta, Alain, et al.
Publicado: (2012)

InferAMP, a python web app for copy number inference from discrete gene-level amplification signals noted in clinical tumor profiling reports
por: Kenny, Paraic A.
Publicado: (2019)

Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array
por: Price, E Magda, et al.
Publicado: (2013)

Impact of SNPs on methylation readouts by Illumina Infinium HumanMethylation450 BeadChip Array: implications for comparative population studies
por: Daca-Roszak, Patrycja, et al.
Publicado: (2015)

NuGO contributions to GenePattern
por: De Groot, P. J., et al.
Publicado: (2008)

Batch effect correction for genome-wide methylation data with Illumina Infinium platform
por: Sun, Zhifu, et al.
Publicado: (2011)

eCAT: Online electronic lab notebook for scientific research
por: Goddard, Nigel H, et al.
Publicado: (2009)

Partitioning of copy-number genotypes in pedigrees
por: Perreault, Louis-Philippe Lemieux, et al.
Publicado: (2010)

Chemotion ELN: an Open Source electronic lab notebook for chemists in academia
por: Tremouilhac, Pierre, et al.
Publicado: (2017)

Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis
por: Reich, Michael, et al.
Publicado: (2023)

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal
por: Eijssen, Lars M.T., et al.
Publicado: (2015)

CONAN: copy number variation analysis software for genome-wide association studies
por: Forer, Lukas, et al.
Publicado: (2010)

Comparison of methylation patterns generated from genomic and cell-line derived DNA using the Illumina Infinium MethylationEPIC BeadChip array
por: Smyth, L. J., et al.
Publicado: (2019)

Laboratory Exercise to Measure Plasmid Copy Number by qPCR
por: David, Benjamin, et al.
Publicado: (2021)

R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips
por: Ritchie, Matthew E., et al.
Publicado: (2009)

Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips
por: Ritchie, Matthew E, et al.
Publicado: (2011)

Identification of DNA methylation biomarkers from Infinium arrays
por: Wessely, Frank, et al.
Publicado: (2012)

A survey of analysis software for array-comparative genomic hybridisation studies to detect copy number variation
por: Karimpour-Fard, Anis, et al.
Publicado: (2010)

SCNVSim: somatic copy number variation and structure variation simulator
por: Qin, Maochun, et al.
Publicado: (2015)

Segmentum: a tool for copy number analysis of cancer genomes
por: Afyounian, Ebrahim, et al.
Publicado: (2017)

Implementation of GenePattern within the Stanford Microarray Database
por: Hubble, Jeremy, et al.
Publicado: (2009)

PANDAseq: paired-end assembler for illumina sequences
por: Masella, Andre P, et al.
Publicado: (2012)

GWAS on your notebook: fast semi-parallel linear and logistic regression for genome-wide association studies
por: Sikorska, Karolina, et al.
Publicado: (2013)

CGHpower: exploring sample size calculations for chromosomal copy number experiments
por: Scheinin, Ilari, et al.
Publicado: (2010)

Copynumber: Efficient algorithms for single- and multi-track copy number segmentation
por: Nilsen, Gro, et al.
Publicado: (2012)

X-CNV: genome-wide prediction of the pathogenicity of copy number variations
por: Zhang, Li, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_hm90ltegjab79p8t1r6l9i9g98