Explore Workflows

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: 3034168d652bfa930ba09af20e473a4564a8010d

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: f225cd99b0e0a5043dd102f8b33a6139fefe9ea4

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: 5463361069e263ad6455858e054c1337b1d9e752

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: 104059e07a2964673e21d371763e33c0afeb2d03

https://github.com/BiodataAnalysisGroup/intro-to-cwl-docker.git

Path: _includes/cwl/1st-workflow.cwl

Branch/Commit ID: 5e18a40c1c17696b0b37ac8d7c11ce9a19f247d9

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

Path: definitions/subworkflows/sequence_to_bqsr_nonhuman.cwl

Branch/Commit ID: 480c438a6a7e78c624712aec01bc4214d2bc179c

AltAnalyze Build Reference Indices ==================================

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

Path: workflows/altanalyze-prepare-genome.cwl

Branch/Commit ID: 8049a781ac4aae579fbd3036fa0bf654532f15be

AltAnalyze ICGS ===============

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

Path: workflows/altanalyze-icgs.cwl

Branch/Commit ID: c9e7f3de7f6ba38ee663bd3f9649e8d7dbac0c86

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

Path: definitions/subworkflows/sv_paired_read_caller_filter.cwl

Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 70e530b65b33301032b7510095d89e497bf5e34e