DNA methylation

• DEBUGGING: BioPortal search
• DEBUGGING: BioPortal lookup

The bioinformatics applications assigned the Biological domain DNA methylation ([ ]) are tabulated below.

Definition:

Synonyms:

Query returned 28 results.

	Biological domain	Bioinformatics method	Input format	Output format
Batman	DNA methylation		GFF
BiQ Analyzer	DNA methylation Epigenomics
BiQ Analyzer HT	DNA methylation Sequencing Epigenetics
Bis-SNP	DNA methylation SNP detection Sequencing Genotyping Epigenetics	Bisulfite mapping SNP calling Methylation calling	BAM	BED WIG VCF BEDGRAPH
Bismark	Genomics DNA methylation Epigenomics	Read mapping Bisulfite mapping Methylation calling	FASTA FASTQ	SAM (or custom)
Bison	DNA methylation Sequencing Epigenetics	Read mapping Bisulfite mapping Methylation calling	FASTQ (Compressed) FASTQ	BAM BEDGRAPH
BRAT	DNA methylation Epigenomics	Bisulfite mapping Mapping
BSMAP	DNA methylation	Read mapping Bisulfite mapping	FASTA FASTQ	SOAP mapping format
BSSim	DNA methylation Sequencing Epigenetics	Modelling and simulation	FASTA	FASTQ SAM Ref
Chipster	DNA methylation ChIP-seq RNA-Seq Immunoprecipitation experiment	Read mapping Peak calling Sequence motif recognition Genome visualisation Sequencing quality control Differential expression analysis Sequence trimming Pathway or network analysis Methylation analysis	FASTQ SAM BAM BED GTF	FASTQ SAM BAM BED GTF
DNAA	DNA methylation SNP detection Structural variation	Sequencing quality control Modelling and simulation Statistical calculation	SAM BAM
EdgeR	DNA methylation ChIP-seq RNA-Seq RNA-Seq quantification Gene expression analysis	Statistical calculation	Table with count data	Table
ERNE	Sequence alignment Genomics DNA methylation Sequencing Epigenetics	Read mapping Bisulfite mapping	FASTQ (Compressed) FASTQ	SAM/BAM
Genedata Expressionist	Genomics Transcriptomics DNA methylation ChIP-seq SNP detection Indel detection RNA-Seq Sequencing Laboratory information management Copy number estimation Epigenetics Gene structure	Read mapping Sequence alignment Annotation Bisulfite mapping Clustering Genome visualisation Sequencing quality control Sequence analysis Statistical calculation Gene expression analysis RNA-Seq analysis	FASTA FASTQ QSEQ SAM BAM GFF BED VCF GTF BedGraph 2bit Nib GDC And many others.
GSNAP	DNA methylation RNA-Seq alignment	Read mapping Bisulfite mapping
KARMA	DNA methylation Sequencing Epigenetics	Read mapping	FASTA FASTQ	SAM
Kismeth	DNA methylation Epigenomics	Bisulfite mapping
MethMarker	DNA methylation Epigenomics
Methpipe	DNA methylation Sequencing Epigenetics	Bisulfite mapping	FASTQ SAM/BAM
MethylCoder	Genomics DNA methylation Epigenomics Sequencing	Read mapping Bisulfite mapping	FASTA FASTQ	SAM TXT Binary
MetMap	DNA methylation
PASH	DNA methylation Epigenomics	Sequence alignment Bisulfite mapping
RMAP	DNA methylation	Read mapping Bisulfite mapping
RUbioSeq	DNA methylation Sequencing Copy number estimation Epigenetics Exome analysis	Variant calling	FASTQ	VCF
Sherman	Genomics DNA methylation Sequencing Epigenetics	Modelling and simulation		FASTQ CSFASTA/CSQUAL (ABI SOLiD)
SOCS	DNA methylation RNA-Seq alignment SNP detection	Read mapping Bisulfite mapping	CSFASTA/CSQUAL (ABI SOLiD)	Delimited Text
SwDMR	DNA methylation Sequencing Epigenetics	Methylation calling	Others	WIG PDF SVG Regions
Syapse	Genomics Transcriptomics DNA methylation ChIP-seq SNP detection Indel detection RNA-Seq Metagenomics DNA transcription Epigenomics Structural variation Population genetics Comparative genomics DNA-Seq Regulatory genomics	Visualisation Sequence analysis Differential expression analysis Ontology comparison Exome analysis Variant classification	VCF