Statistical genomics. Methods and protocols
DOI10.1007/978-1-4939-3578-9zbMath1346.92003MaRDI QIDQ293809
No author found.
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
machine learning; sequence alignment; RNA-seq; meta-analysis; experimental design; next generation sequencing; BEDOPS; cancer genome atlas (TCGA); cell specific regulatory code; ChiP-seq; differential expression analysis; edgeR; exploratory analysis; gene expression omnibus; genome contact interaction enrichment analysis; genomic ranges; GMAP; GSNAP; Gviz; large scale DNAseq data; NGS-QC; oligonucleotide arrays; power calculation; R/Bioconductor; visualizing genomic data; WEKA
62P10: Applications of statistics to biology and medical sciences; meta analysis
92B15: General biostatistics
62B15: Theory of statistical experiments
62K05: Optimal statistical designs
62F15: Bayesian inference
92D10: Genetics and epigenetics
92-02: Research exposition (monographs, survey articles) pertaining to biology
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
