Computational Genomics with R

DOI10.1201/9780429084317zbMath1482.92002OpenAlexW3107402760MaRDI QIDQ5151092

Altuna Akalin

Publication date: 16 February 2021

Full work available at URL: https://doi.org/10.1201/9780429084317

zbMATH Keywords

Rregulationclusteringestimatesdata analysislogistic regressionregressiondecision treespredictive modellingvisualisationdimensionality reductionspreadstatisticsrandom forestsdifferential gene expressioncross validationgenomicscentral tendencyunsupervised machine learninghigh throughput sequencingRNAseqdata pre-processingcentral dogmabisulphite sequencing dataChIPseq analysisclustering using latent factorsfastq/fasta formatgenome arithmeticggplotmulti-omics analysismultiple testing correctionspeak callingread processingsupervise machine learningvisualisation on genome browser

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10) Research exposition (monographs, survey articles) pertaining to biology (92-02)

Uses Software

• R
• STAR
• Silhouettes
• Bioconductor
• CRAN
• ggplot2
• FactoMineR
• edgeR
• RStudio
• AUGUSTUS
• GATK
• KEGG
• AS 136
• ShortRead
• FastQC
• Trimmomatic
• TopHat
• BSgenome
• Gviz
• JASPAR
• TFBSTools
• tidyverse
• pheatmap
• XGBoost
• sva
• methylKit
• Bismark
• gage
• DALEX
• Tabix
• HISAT
• systemPipeR
• QuasR
• ChromHMM
• GenomicRanges
• Bowtie 2
• Rtsne
• Salmon
• SMOTE
• PePr
• Rqc
• Rsamtools
• BiocManager
• compGenomRData
• genomation
• ODIN
• gmapR
• normr
• deFuse
• GISTIC2.0
• MAnorm
• GenomicAlignments
• ggbio
• Rbowtie
• Trim Galore
• rGADEM
• rGREAT
• MethylSeekR
• BiSeq
• iClusterPlus
• intePareto

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