Explore Workflows

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Graph Name Retrieved From View
workflow graph DiffBind - Differential Binding Analysis of ChIP-Seq Peak Data

Differential Binding Analysis of ChIP-Seq Peak Data --------------------------------------------------- DiffBind processes ChIP-Seq data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously, representing different ChIP experiments (antibodies, transcription factor and/or histone marks, experimental conditions, replicates) as well as managing the results of multiple peak callers. For more information please refer to: ------------------------------------- Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, Ali S, Chin S, Palmieri C, Caldas C, Carroll JS (2012). “Differential oestrogen receptor binding is associated with clinical outcome in breast cancer.” Nature, 481, -4.

 https://github.com/datirium/workflows.git

Path: workflows/diffbind.cwl

Branch/Commit ID: 17a4a68b20e0af656e09714c1f39fe761b518686
workflow graph count-lines6-wf.cwl

https://github.com/common-workflow-language/common-workflow-language.git

Path: v1.0/v1.0/count-lines6-wf.cwl

Branch/Commit ID: 4fe434e969c93c94b690ba72db295d9d52a6f576
workflow graph Build Bismark indices

Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.

 https://github.com/datirium/workflows.git

Path: workflows/bismark-index.cwl

Branch/Commit ID: 17a4a68b20e0af656e09714c1f39fe761b518686
workflow graph WGS QC workflow nonhuman

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/qc_wgs_nonhuman.cwl

Branch/Commit ID: b9e7392e72506cadd898a6ac4db330baf6535ab6
workflow graph prepare_reference.cwl

https://github.com/kids-first/kf-alignment-workflow.git

Path: subworkflows/prepare_reference.cwl

Branch/Commit ID: 09c05e788df9cd77cead39892fd02140faa765a8
workflow graph Subworkflow to allow calling different SV callers which require bam files as inputs

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/single_sample_sv_callers.cwl

Branch/Commit ID: 3a822294da63b4e19446a285e2fef075e23cf3d0
workflow graph align_merge_sas

https://github.com/ncbi/pgap.git

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: be465ad19b07378f3f863f2c4e0019b420c859f2
workflow graph kmer_top_n_extract

https://github.com/ncbi-gpipe/pgap.git

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: b360e89d85d83ba3b863bf86074c0ec7e5c58f48
workflow graph taxonomy_check_16S

https://github.com/ncbi/pgap.git

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: b12ec8c8e832151033b9e6c0a76a3c3df18d45da
workflow graph Detect Docm variants

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: 480c438a6a7e78c624712aec01bc4214d2bc179c