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Table 2 Mapping ISA configurations to BiocViews

From: The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again

ISA Configuration File

ISA measurement

BiocViews

ISA technology

BiocViews

cellcount_flowcytometry

cell counting

 

flow cytometry

FlowCytometry

cellsorting_flowcyt

cell sorting

 

flow cytometry

FlowCytometry

clinical_chemistry

clinical chemistry analysis

   

copynumvariation_micro

copy number variation profiling

CopyNumberVariants

DNA microarray

Microarray, aCGH

dnamethylation_micro

DNA methylation profiling

DNAMethylation

DNA microarray

Microarray, ChIPchip, CpGIsland, Methylseq

dnamethylation_seq

DNA methylation profiling

DNAMethylation

nucleotide sequencing

Sequencing, ChIPseq, CpGIsland, Methylseq

envgen survey_seq

environmental gene survey

 

nucleotide sequencing

Sequencing

genome_seq

genome sequencing

 

nucleotide sequencing

Sequencing

hematology

hematology

   

heterozygosity_micro

loss of heterozygosity profiling

SNP, CopyNumber Variants

DNA microarray

Microarray

histology

histology

   

histonemodification_seq

histone modification profiling

Regulation

nucleotide sequencing

Sequencing, ChIPseq

metaboliteprofiling_ms

metabolite profiling

Metabolomics

mass spectrometry

MassSpectrometry

metaboliteprofiling_nmr

metabolite profiling

Metabolomics

NMR spectroscopy

 

metagenome_seq

metagenome sequencing

 

nucleotide sequencing

Sequencing

ppi_detection_micro

protein-protein interaction detection

 

protein microarray

Microarray

protein_dna_binding_ident_micro

protein-DNA binding site identification

Regulation

DNA microarray

Microarray, ChIPchip

protein_dna_binding_ident_seq

protein-DNA binding site identification

Regulation

nucleotide sequencing

Sequencing, ChIPseq

protein expression_ge

protein expression profiling

Proteomics

gel electrophoresis

 

protein expression_micro

protein expression profiling

Proteomics

protein microarray

Microarray

protein expression_ms

protein expression profiling

Proteomics

mass spectrometry

MassSpectrometry, Proteomics

proteinident_ms

protein identification

 

mass spectrometry

MassSpectrometry, Proteomics

snpanalysis_micro

SNP analysis

SNP

DNA microarray

Microarray, GeneticVariability

studySample

    

tfbsident_micro

transcription factor binding site identification

Regulation

DNA microarray

Microarray, ChIPchip

tfbsident_seq

transcription factor binding site identification

Regulation

nucleotide sequencing

Sequencing, ChIPseq

transcription_micro

transcription profiling

Transcription, GeneExpression

DNA microarray

Microarray, DifferentialExpression, ExonArray

transcription_rtpcr

transcription profiling

Transcription, GeneExpression, DifferentialExpression

real time PCR

qPCR

transcription_seq

transcription profiling

Transcription, GeneExpression

nucleotide sequencing

Sequencing, DifferentialExpression, RNAseq