Copy number estimation

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The bioinformatics applications assigned the Biological domain Copy number estimation ([ ]) are tabulated below.

Definition:

Synonyms:

Query returned 25 results.

	Biological domain	Bioinformatics method	Input format	Output format
ADTEx	Copy number estimation Exome analysis Cancer biology Next Generation Sequencing	Statistical calculation	BAM BED	Tab-delimited file
CEQer	Copy number estimation Genetic variation analysis Exome analysis		Pileup SAM/BAM	Graphical
CLEVER	Genomics Structural variation Copy number estimation		BAM	Tab separated
CNANorm	Genomics Copy number estimation Cancer biology	Peak calling Standardisation and normalisation	SAM BAM Delimited Text	Delimited Text
CnD	Copy number estimation
CNVer	Structural variation Copy number estimation		FASTA
CNVkit	Structural variation Copy number estimation	Variant calling	BAM BED	BED-like
CNVnator	Genotyping Copy number estimation
CNVseq	Copy number estimation
Contra	Genomics Sequencing Copy number estimation Cancer biology		BAM BED	VCF Tab-delimited
CopySeq	Structural variation Genotyping Personalised medicine Copy number estimation		BAM	Tab-delimited file
ERDS	Copy number estimation
ExomeCNV	Exome capture Copy number estimation
ExomeCopy	Copy number estimation Exome and whole genome variant detection Exome analysis		BAM
FREEC	Copy number estimation		SAM BAM BED Eland SOAP Bowtie Arachne binary Psl
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.
Golden Helix	Genomics SNP detection Epigenomics Sequencing Copy number estimation Data handling	Annotation Genome visualisation Sequencing quality control Sequence contamination filtering Variant calling Statistical calculation Collapsing methods Variant classification
JointSLM	Copy number estimation
MrCaNaVaR	Genomics Personalised medicine Copy number estimation	Read depth analysis	SAM	BED (copy numbers)
Patchwork	Structural variation Copy number estimation		BAM VCF Pileup	CSV PNG JPG
ReadDepth	Copy number estimation
RefCov	Copy number estimation
RUbioSeq	DNA methylation Sequencing Copy number estimation Epigenetics Exome analysis	Variant calling	FASTQ	VCF
SeqSeg	Copy number estimation
SWT	Copy number estimation