Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph Unaligned to aligned BAM

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

Path: definitions/subworkflows/align.cwl

Branch/Commit ID: 889a077a20c0fdb01f4ed97aa4bc40f920c37a1a
workflow graph GSEApy - Gene Set Enrichment Analysis in Python

GSEAPY: Gene Set Enrichment Analysis in Python ============================================== Gene Set Enrichment Analysis is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). GSEA requires as input an expression dataset, which contains expression profiles for multiple samples. While the software supports multiple input file formats for these datasets, the tab-delimited GCT format is the most common. The first column of the GCT file contains feature identifiers (gene ids or symbols in the case of data derived from RNA-Seq experiments). The second column contains a description of the feature; this column is ignored by GSEA and may be filled with “NA”s. Subsequent columns contain the expression values for each feature, with one sample's expression value per column. It is important to note that there are no hard and fast rules regarding how a GCT file's expression values are derived. The important point is that they are comparable to one another across features within a sample and comparable to one another across samples. Tools such as DESeq2 can be made to produce properly normalized data (normalized counts) which are compatible with GSEA.

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

Path: workflows/gseapy.cwl

Branch/Commit ID: 935a78f1aff757f977de4e3672aefead3b23606b
workflow graph bacterial_orthology

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

Path: bacterial_orthology/wf_bacterial_orthology.cwl

Branch/Commit ID: 2801ce53744a085580a8de91cd007c45146b51e8
workflow graph wf3.cwl

https://github.com/RenskeW/cwlprov-provenance.git

Path: sl_prov_question/scenario3/wf3.cwl

Branch/Commit ID: 250f2383beddb8e0bdfcaecf169df488250d365e
workflow graph genomics-workspace-genome.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_genomicsWorkspace/genomics-workspace-genome.cwl

Branch/Commit ID: 677d79c721ad5f7a7e09b693d7f3fe2da70826e2
workflow graph workflow.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: flow_download/workflow.cwl

Branch/Commit ID: 8b8c6dd16e06b43fbb50f1c0821856a31f1bbbc5
workflow graph Filter Protein Seeds; Find ProSplign Alignments

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

Path: protein_alignment/wf_compart_filter_prosplign.cwl

Branch/Commit ID: 505b91e41741ccbcd5ebd2b6a09a3be604f9ece3
workflow graph workflow.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: flow_apollo2_data_processing/processing/workflow.cwl

Branch/Commit ID: 8b8c6dd16e06b43fbb50f1c0821856a31f1bbbc5
workflow graph Unaligned bam to sorted, markduped bam

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

Path: definitions/subworkflows/align_sort_markdup.cwl

Branch/Commit ID: f9600f9959acdc30259ba7e64de61104c9b01f0b
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 505b91e41741ccbcd5ebd2b6a09a3be604f9ece3