Explore Workflows

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: 5463361069e263ad6455858e054c1337b1d9e752

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

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: 7cee09fb3e33c851e4e1dfc965c558b82290a785

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

Path: steps/bulk_process.cwl

Branch/Commit ID: 904fbfbbee5f867a6b642cb225c02386549c49f6

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

Path: tests/wf/scatterfail.cwl

Branch/Commit ID: 89ccbfc53ff3bb6abe2eb90bb7e0091c54c18f5c

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

Path: definitions/subworkflows/bam_to_bqsr_no_dup_marking.cwl

Branch/Commit ID: 742dbafb5fb103d8578f48a0576c14dd8dae3b2a

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: 233f026ffce240071edda526391be0c03186fce8

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

Path: definitions/subworkflows/pvacseq.cwl

Branch/Commit ID: 3042812447d9e8889c6118986490e9c9b9b13223

What is MAnorm? -------------- MAnorm is a robust model for quantitative comparison of ChIP-Seq data sets of TFs (transcription factors) or epigenetic modifications and you can use it for: * Normalization of two ChIP-seq samples * Quantitative comparison (differential analysis) of two ChIP-seq samples * Evaluating the overlap enrichment of the protein binding sites(peaks) * Elucidating underlying mechanisms of cell-type specific gene regulation How MAnorm works? ---------------- MAnorm uses common peaks of two samples as a reference to build the rescaling model for normalization, which is based on the empirical assumption that if a chromatin-associated protein has a substantial number of peaks shared in two conditions, the binding at these common regions will tend to be determined by similar mechanisms, and thus should exhibit similar global binding intensities across samples. The observed differences on common peaks are presumed to reflect the scaling relationship of ChIP-Seq signals between two samples, which can be applied to all peaks. What do the inputs mean? ---------------- ### General **Experiment short name/Alias** * short name for you experiment to identify among the others **ChIP-Seq SE sample 1** * previously analyzed ChIP-Seq single-read experiment to be used as Sample 1 **ChIP-Seq SE sample 2** * previously analyzed ChIP-Seq single-read experiment to be used as Sample 2 **Genome** * Reference genome to be used for gene assigning ### Advanced **Reads shift size for sample 1** * This value is used to shift reads towards 3' direction to determine the precise binding site. Set as half of the fragment length. Default 100 **Reads shift size for sample 2** * This value is used to shift reads towards 5' direction to determine the precise binding site. Set as half of the fragment length. Default 100 **M-value (log2-ratio) cutoff** * Absolute M-value (log2-ratio) cutoff to define biased (differential binding) peaks. Default: 1.0 **P-value cutoff** * P-value cutoff to define biased peaks. Default: 0.01 **Window size** * Window size to count reads and calculate read densities. 2000 is recommended for sharp histone marks like H3K4me3 and H3K27ac, and 1000 for TFs or DNase-seq. Default: 2000

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

Path: workflows/manorm-se.cwl

Branch/Commit ID: 4360fb2e778ecee42e5f78f83b78c65ab3a2b1df

https://github.com/KBNLresearch/ochre.git

Path: ochre/cwl/word-mapping-test-files-wf.cwl

Branch/Commit ID: a62bf3b31df83784c017d30a83ed8e01d454bf1c

Packed ID: main

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

Path: v1.0/v1.0/io-int-default-wf.cwl

Branch/Commit ID: e67f19d8a713759d761ecad050966d1eb043b85c