Explore Workflows

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Graph Name Retrieved From View
workflow graph Seed Protein Alignments

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

Path: protein_alignment/wf_seed_1.cwl

Branch/Commit ID: c17cac4c046f8ba2b8574a121c44a72d2e6b27e6
workflow graph ROSE: rank ordering of super-enhancers

Super-enhancers, consist of clusters of enhancers that are densely occupied by the master regulators and Mediator. Super-enhancers differ from typical enhancers in size, transcription factor density and content, ability to activate transcription, and sensitivity to perturbation. Use to create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)

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

Path: workflows/super-enhancer.cwl

Branch/Commit ID: cc6fa135d04737fdde3b4414d6e214cf8c812f6e
workflow graph Filter ChIP/ATAC/cut&run/diffbind peaks for Tag Density Profile or Motif Enrichment analyses

Filters ChIP/ATAC/cut&run/diffbind peaks with the neatest genes assigned for Tag Density Profile or Motif Enrichment analyses ============================================================================================================ Tool filters output from any ChIP/ATAC/cut&run/diffbind pipeline to create a file with regions of interest for Tag Density Profile or Motif Enrichment analyses. Peaks with duplicated coordinates are discarded.

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

Path: workflows/filter-peaks-for-heatmap.cwl

Branch/Commit ID: d76110e0bfc40c874f82e37cef6451d74df4f908
workflow graph Filter Protein Alignments

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

Path: protein_alignment/wf_align_filter.cwl

Branch/Commit ID: c17cac4c046f8ba2b8574a121c44a72d2e6b27e6
workflow graph Cell Ranger Count (RNA+ATAC)

Cell Ranger Count (RNA+ATAC) Quantifies single-cell gene expression and chromatin accessibility of the sequencing data from a single 10x Genomics library in a combined manner. The results of this workflow are primarily used in either “Single-Cell Multiome ATAC and RNA-Seq Filtering Analysis” or “Cell Ranger Aggregate (RNA+ATAC)” pipelines.

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

Path: workflows/cellranger-arc-count.cwl

Branch/Commit ID: b4d578c2ba4713a5a22163d9f8c7105acda1f22e
workflow graph tt_kmer_top_n.cwl

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: 369e2b6c7f4db75099d258729dec1326f55d2cc5
workflow graph kmer_ref_compare_wnode

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

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: 369e2b6c7f4db75099d258729dec1326f55d2cc5
workflow graph tt_kmer_compare_wnode

Pairwise comparison

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: 369e2b6c7f4db75099d258729dec1326f55d2cc5
workflow graph kmer_build_tree

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: 369e2b6c7f4db75099d258729dec1326f55d2cc5
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 369e2b6c7f4db75099d258729dec1326f55d2cc5