Peak calling

Query returned 31 results.

	Biological domain	Bioinformatics method	Input format	Output format
AREM	ChIP-seq	Read mapping Peak calling	SAM Bowtie	BED
Bcbio-nextgen	Workflows	Read mapping Sequence alignment Peak calling Sequence motif recognition Genotyping Sequencing quality control Differential expression analysis Sequence trimming Filtering Genomic region matching	FASTQ	FASTQ SAM BAM BED PDF VCF
CexoR	ChIP-exo	Peak calling	Bam	BED GRanges R data.frame
CHiCAGO	Epigenomics	Peak calling	BAM	SeqMonk IBed WashU
ChIP-Seq (application)	ChIP-seq	Read mapping Peak calling	BAM GFF BED SGA FPS	GFF BED SGA FPS
ChIPmeta	ChIP-seq ChIP-on-chip Transcription factors and regulatory sites	Peak calling
CHiPSeq	ChIP-seq	Peak calling
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
CNANorm	Genomics Copy number estimation Cancer biology	Peak calling Standardisation and normalisation	SAM BAM Delimited Text	Delimited Text
DNaseR	DNase-seq	Peak calling Nucleic acid sequence feature detection	BAM	GRanges R data.frame
EaSeq	ChIP-Seq	Visualisation Peak calling Viewer Clustering Integrated solution Genome visualisation Analysis Biological interpretation Regression analysis Correlation Filtering Genomic region matching Format conversion Read summarisation Enrichment Global test Visualisation Quality assessement And more...	Compressed/uncompressed CSV Delimited Text BedGraph Bed Customizable Bam Wig Aln	Compressed/uncompressed Delimited Text BedGraph Bed Wig Aln Tif .eas (Custom Session file format)
FindPeaks 3.1	ChIP-seq	Peak calling	ELAND MAQ BED	WIG Peaks
FindPeaks 4.0 (Vancouver Short Read Package)	Genomics SNP detection	Peak calling Formatting Sequence alignment analysis	FASTA SAM BED Eland Maq Bowtie Mapview	GFF BED WIG Peaks ACE PNG Regions
GEM	ChIP-seq	Peak calling Sequence motif discovery	SAM BAM ELAND BED Bowtie
GeneProf	ChIP-seq RNA-Seq	Read mapping Visualisation Peak calling Sequencing quality control Differential expression analysis	FASTA (Compressed) FASTQ Others (Compressed) FASTA Table with count data Tab-delimited	FASTA FASTQ BED WIG XLS TXT HTML Tab-delimited Images
GenomicTools	Genomics ChIP-seq RNA-Seq	Peak calling Heat map generation Genome comparison	GFF BED SAM/BAM	SAM GFF BED
GenoMiner	Sequence assembly Sequence assembly (de novo assembly) ChIP-seq RNA-Seq	Sequence assembly Sequence alignment Peak calling Sequence error correction Plotting and rendering Mutation detection Gene expression profiling
GPS	Genomics ChIP-seq Epigenomics Transcription factors and regulatory sites	Peak calling	ELAND BED Bowtie SAM/BAM
HINT	Epigenomics Transcription factors and regulatory sites Regulatory genomics	Peak calling Nucleic acid sequence feature detection	BAM BED	BED
Lasergene	Sequence assembly (de novo assembly) Genomics SNP detection Indel detection Mapping Transcription factors and regulatory sites Sequence analysis Phylogenetics Protein structure analysis	Sequence assembly Read mapping Sequence alignment Peak calling Annotation Sequence analysis Scaffolding Sequence alignment analysis Chromatogram visualisation PCR primer design
MACS	ChIP-seq	Peak calling	SAM BAM ELAND BED	BED WIG
MotifLab	ChIP-seq Sequence motifs Transcription factors and regulatory sites Sequence analysis Gene regulation	Visualisation Peak calling Genome visualisation Sequence contamination filtering Sequence motif discovery Format conversion	FASTA GFF BED WIG CSV Delimited Text Others GTF Custom MEME Bioprospector Custom Motif format BedGraph Plain text BigWig Excel 2bit BigBed JASPAR XMS TRANSFAC	FASTA GFF BED WIG CSV Delimited Text HTML Others GTF Custom MEME Bioprospector Custom Motif format BedGraph Plain text Excel JASPAR XMS TRANSFAC
MultiPSQ	Phylogenetics Microbial Surveillance Public health and epidemiology	Peak calling Classification Peptide mass fingerprint
NarrowPeaks	ChIP-seq	Peak calling Differential Binding	WIG BigWig	BED GRanges
NucleR	ChIP-seq Epigenomics ChIP-on-chip DNA packaging	Peak calling Annotation	ShortRead BioConductor	BED WIG BioConductor
ODIN	Genomics Regulatory genomics	Peak calling	BAM BED	BED BigWig
PeakRanger	ChIP-seq	Peak calling	BED Bowtie SAM/BAM	BED
QSeq	ChIP-seq RNA-Seq Regulatory RNA	Sequence alignment Visualisation Peak calling
SeqSite	ChIP-seq	Peak calling	BED	BED Bar
Sissrs	ChIP-seq	Peak calling	BED	BED WIG
SPP	Genomics ChIP-seq	Peak calling	ELAND MAQ Bowtie Arachne binary