Statistical genomics. Methods and protocols

DOI10.1007/978-1-4939-3578-9MaRDI QIDQ293809zbMATH OpenOpenAlexFDO

Authors

Publication date 9 June 2016

Published in Methods in Molecular Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-1-4939-3578-9

zbMATH Keywords

experimental designmachine learningmeta-analysisRNA-seqnext generation sequencingBEDOPScancer genome atlas (TCGA)cell specific regulatory codeChiP-seqdifferential expression analysisedgeRexploratory analysisgene expression omnibusgenome contact interaction enrichment analysisgenomic rangesGMAPGSNAPGvizlarge scale DNAseq dataNGS-QColigonucleotide arrayspower calculationR/Bioconductorsequence alignmentvisualizing genomic dataWEKA

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Optimal statistical designs (62K05) General biostatistics (92B15) Genetics and epigenetics (92D10) Theory of statistical experiments (62B15) Research exposition (monographs, survey articles) pertaining to biology (92-02)

Recommendations

• Principles of statistical genomics
• Handbook of Statistical Genomics
• Statistics in human genetics and molecular biology.
• Statistical methods for microarray data analysis. Methods and protocols
• Primer to analysis of genomic data using R

Cited in

(12)

• Scalable genomics with \texttt{R} and bioconductor
• Statistics in molecular biology and genetics. Selected proceedings of the Joint AMS-IMS-SIAM summer conference on statistics in molecular biology, Seattle, WA, USA, June 22--26, 1997
• Handbook of Statistical Genomics
• Transcriptome analysis. Introduction and examples from the neurosciences
• Principles of statistical genomics
• Computational exome and genome analysis
• Primer to analysis of genomic data using R
• Computational and Statistical Approaches to Genomics
• An overview of recent developments in genomics and associated statistical methods
• Mini-workshop: Recent developments in statistical methods with applications to genetics and genomics. Abstracts from the mini-workshop held November 8--14, 2015
• Computational genomics with R. With the assistance of Verdan Franke, Bora Uyar and Jonathan Ronen
• Statistical analysis of next generation sequencing data

Describes a project that uses

Uses Software

• ROAST
• featureCounts
• Rsubread
• recount
• PROPER
• GenomeGraphs
• Rtracklayer
• Gviz
• GeneHug-GEPIS
• VariantAnnotation
• SSAHA
• VariantTools
• GSNAP
• BEDOPS
• Genoviz
• Cutadapt
• BEDTools
• NGS-QC
• pyDNase
• DREME
• FIMO
• F-Seq
• VarSifter
• ANNOVAR
• MEDIPS
• GSVA
• DAVID
• curatedOvarianData
• GEOmetadb
• Oncomine
• inSilicoDb
• GeneSigDB
• ExpTreeDB
• GEOquery
• AnnotationForge
• BSgenome
• OrganismDbi
• AnnotationHub
• biomaRt
• GenomicFeatures
• CellMiner
• IGV
• GMAP
• BioMart
• NGS QC Toolkit
• TopHat
• FastQC
• Galaxy
• HTSeq
• BLAT
• MEME
• VCFtools
• Biostrings
• KEGG
• metafor
• C4.5
• snpStats
• Sweave
• Soap
• RankProd
• AnnotationDbi
• rmarkdown
• shiny
• knitr
• edgeR
• WEKA
• oligo
• Bioconductor
• STAR
• R

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