Explore Workflows

https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git

Path: steps/bulk_process.cwl

Branch/Commit ID: 5465f666aac446a6d66fed1819e48a79395f6b02

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

Path: definitions/subworkflows/align.cwl

Branch/Commit ID: 1437aed13d240fd624f78df2c7efb096c5079d73

For a given Zenodo community, retrieve its repository records as Zenodo JSON and (eventually) schema.org JSON-LD and DataCite v4 XML.

https://github.com/stain/ro-index-paper.git

Path: code/data-gathering/workflows/zenodo-records.cwl

Branch/Commit ID: eba15168698e62150c10924bd7b2fa1ff1f0c85a

Runs RNA-Seq BioWardrobe basic analysis with single-end data file.

https://github.com/Barski-lab/workflows.git

Path: workflows/trim-rnaseq-se.cwl

Branch/Commit ID: 9a03dbe8829ca649814d9c8bd11fe3a673750a95

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

Path: definitions/subworkflows/cram_to_cnvkit.cwl

Branch/Commit ID: c6bbd4cdd612b3b5cc6e9000df4800c21e192bf5

Reverse the lines in a document, then sort those lines.

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

Path: tests/wf/revsort.cwl

Branch/Commit ID: 63f539ba60e91f0cb3ce7cda2c5da5c65525c375

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: 0805e8e0d358136468e0a9f49e06005e41965adc

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. Documents ============================================== - GSEA Home Page: https://www.gsea-msigdb.org/gsea/index.jsp - Results Interpretation: https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideTEXT.htm#_Interpreting_GSEA_Results - GSEA User Guide: https://gseapy.readthedocs.io/en/latest/faq.html - GSEAPY Docs: https://gseapy.readthedocs.io/en/latest/introduction.html References ============================================== - Subramanian, Tamayo, et al. (2005, PNAS), https://www.pnas.org/content/102/43/15545 - Mootha, Lindgren, et al. (2003, Nature Genetics), http://www.nature.com/ng/journal/v34/n3/abs/ng1180.html - Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013; 128(14). - Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research. 2016; gkw377 . - Xie Z, Bailey A, Kuleshov MV, Clarke DJB., Evangelista JE, Jenkins SL, Lachmann A, Wojciechowicz ML, Kropiwnicki E, Jagodnik KM, Jeon M, & Ma’ayan A. Gene set knowledge discovery with Enrichr. Current Protocols, 1, e90. 2021. doi: 10.1002/cpz1.90

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

Path: workflows/gseapy.cwl

Branch/Commit ID: b4d578c2ba4713a5a22163d9f8c7105acda1f22e

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

Path: protein_alignment/wf_protein_alignment.cwl

Branch/Commit ID: ce433f771ebf5677c9f40858e2ae91b1a7e75d30

https://github.com/common-workflow-lab/wdl-cwl-translator.git

Path: wdl2cwl/tests/cwl_files/struct_output.cwl

Branch/Commit ID: 81d4bdaecebaa843903b40834cb15e350aa047e8