Explore Workflows

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: 5e7385b8cfa4ddae822fff37b6bd22eb0370b389

https://github.com/lrodrin/vre-process_cwl-executor.git

Path: tests/basic/data/workflows/basic_example.cwl

Branch/Commit ID: f4bbddb93cb38e50b8c2eb89d43b926138fa3455

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/functional_analysis.cwl

Branch/Commit ID: 25129f55226dee595ef941edc24d3c44414e0523

https://github.com/cancerit/workflow-seq-import.git

Path: cwls/chksum_seqval_wf_paired_fq.cwl

Branch/Commit ID: 4765cf6955bdce1320fdead7fe51be0e1b63c33d

https://github.com/cr-ste-justine/chujs-alignment-workflow.git

Path: workflows/wgsp_alignment_fq_wf.cwl

Branch/Commit ID: c8255e2aab840f671d9f142d74f915c76415ff51

Devel version of Single-Cell Preprocessing Pipeline ===================================================

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

Path: workflows/single-cell-preprocess.cwl

Branch/Commit ID: 5561f7ee11dd74848680351411a19aa87b13d27b

https://github.com/cancerit/workflow-seq-import.git

Path: cwls/validate_interleaved_fq.cwl

Branch/Commit ID: 4765cf6955bdce1320fdead7fe51be0e1b63c33d

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/cmsearch-multimodel.cwl

Branch/Commit ID: 25129f55226dee595ef941edc24d3c44414e0523

Assemble a set of reads using SKESA

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

Path: assemble.cwl

Branch/Commit ID: 7c8eb4d23c3c9859f57421643710c0b6d57b606c

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/extract_readgroup_fastq_pe.cwl

Branch/Commit ID: 1046947f8d2923e6563b3aceac9e435554c5bea1