Statistical genomics. Methods and protocols

DOI10.1007/978-1-4939-3578-9zbMath1346.92003OpenAlexW4252732282MaRDI QIDQ293809

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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

machine learningsequence alignmentRNA-seqmeta-analysisexperimental designnext 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/Bioconductorvisualizing genomic dataWEKA

Mathematics Subject Classification ID

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

Uses Software

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

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