Computational Genomics with R

DOI10.1201/9780429084317zbMath1482.92002MaRDI QIDQ5151092

Altuna Akalin

Publication date: 16 February 2021

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

zbMATH Keywords

R; regulation; clustering; estimates; data analysis; logistic regression; regression; decision trees; predictive modelling; visualisation; dimensionality reduction; spread; statistics; random forests; differential gene expression; cross validation; genomics; central tendency; unsupervised machine learning; high throughput sequencing; RNAseq; data pre-processing; central dogma; bisulphite sequencing data; ChIPseq analysis; clustering using latent factors; fastq/fasta format; genome arithmetic; ggplot; multi-omics analysis; multiple testing corrections; peak calling; read processing; supervise machine learning; visualisation on genome browser

Mathematics Subject Classification ID

62P10: Applications of statistics to biology and medical sciences; meta analysis

92D10: Genetics and epigenetics

92-02: Research exposition (monographs, survey articles) pertaining to biology

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