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Graph Name Retrieved From View
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: 4360fb2e778ecee42e5f78f83b78c65ab3a2b1df
workflow graph Run genomic CMsearch

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

Path: bacterial_noncoding/wf_gcmsearch.cwl

Branch/Commit ID: 7cee09fb3e33c851e4e1dfc965c558b82290a785
workflow graph umi duplex alignment workflow

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

Path: definitions/subworkflows/duplex_alignment.cwl

Branch/Commit ID: ece70ac30cd87100a70f7dc64d08fa72724e9416
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: a539d600357a48a558daf43fc41a89aae79f9e86
workflow graph bam to trimmed fastqs

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

Path: definitions/subworkflows/bam_to_trimmed_fastq.cwl

Branch/Commit ID: ece70ac30cd87100a70f7dc64d08fa72724e9416
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_qc.cwl

Branch/Commit ID: 4aba7c6591c2f1ebd827a36d325a58738c429bea
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: a539d600357a48a558daf43fc41a89aae79f9e86
workflow graph BAM to BEDPE

Comvert BAM to BEDPE and compress the output

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/File-formats/bamtobedpe-gzip.cwl

Branch/Commit ID: 06501cfc314e36749043431e67c2990966b452e0
workflow graph Nested workflow example

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

Path: tests/wf/nested.cwl

Branch/Commit ID: c7c379948c02ba8f048d157f06eb903b1bda9894
workflow graph cluster_blastp_wnode and gpx_qdump combined

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

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: bc0f1f147231c759fb2d5ff99f41b2667a5588ad