Explore Workflows

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Graph	Name	Retrieved From	View
	Motif Finding with HOMER with target and background regions from peaks Motif Finding with HOMER with target and background regions from peaks --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/)	https://github.com/datirium/workflows.git Path: workflows/homer-motif-analysis-peak.cwl Branch/Commit ID: a1f6ca50fcb0881781b3ba0306dd61ebf555eaba
	group-isoforms-batch.cwl Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.	https://github.com/datirium/workflows.git Path: tools/group-isoforms-batch.cwl Branch/Commit ID: 4a5c59829ff8b9f3c843e66e3c675dcd9c689ed5
	assm_assm_blastn_wnode	https://github.com/ncbi/pgap.git Path: task_types/tt_assm_assm_blastn_wnode.cwl Branch/Commit ID: a34f47d1e37af51e387ecdfa5c3047f106c1146b
	Unaligned BAM to BQSR and VCF	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/bam_to_bqsr_no_dup_marking.cwl Branch/Commit ID: f77a920bcc73f6cfdb091eed75a149d02cd8a263
	umi molecular alignment workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/molecular_alignment.cwl Branch/Commit ID: a7838a5ca72b25db5c2af20a15f34303a839980e
	count-lines3-wf.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/count-lines3-wf.cwl Branch/Commit ID: 596aab620489cd2611f4bc1d9a4fc914ddf34514
	Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)	https://github.com/ncbi/pgap.git Path: bacterial_annot/wf_bacterial_annot_pass1.cwl Branch/Commit ID: da35c7b700912dd3643e3dd2c5c96b7be3a4edad
	Alignment without BQSR	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/sequence_to_bqsr_mouse.cwl Branch/Commit ID: f77a920bcc73f6cfdb091eed75a149d02cd8a263
	exome alignment and tumor-only variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/tumor_only_exome.cwl Branch/Commit ID: 061d3a2fbcd8a1c39c0b38c549e528deb24a9d54
	Varscan Workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/varscan_germline.cwl Branch/Commit ID: a7838a5ca72b25db5c2af20a15f34303a839980e