Explore Workflows

https://github.com/aheinzel/tmp_rhapsody_for_cwl_vis.git

Path: wf.cwl

Branch/Commit ID: c8d75785fd6accf3b47d1f9ee056675611e22e61

Packed ID: VDJ_Assemble_and_Annotate_Contigs_IG.cwl

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

Path: definitions/pipelines/panel_of_normals.cwl

Branch/Commit ID: 641bdeffd942f5121e19626a094c8633386ad546

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

Path: definitions/pipelines/exome_alignment_mouse.cwl

Branch/Commit ID: 1560e7817fdb71d58aca7f98aba68809d840ade1

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

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: 0788fbf0432567fd4fc131c6757904841ccd72ba

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

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: 66b5bc323dcd23e1b2c14bf4783babf0f15ca43b

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

Path: cwltool/schemas/v1.0/v1.0/conflict-wf.cwl

Branch/Commit ID: bf93dd3e6e3261e1455530984ce045f283535d17

Packed ID: collision

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: e238d1756f1db35571e84d72e1699e5d1540f10c

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

Path: definitions/subworkflows/bam_to_bqsr.cwl

Branch/Commit ID: 5677d6df78453e62d2e78ab485f216feaef91681

This workflow performs calibrations, related to the molecular content of the atmosphere. To be updated...

https://gitlab.cta-observatory.org/cta-computing/dpps/dpps-workflows.git

Path: workflows/calibpipe/AtmosphericCalibrations/MolecularAtmosphere/uc-dpps-cp-110.cwl

Branch/Commit ID: 76f7c25c0472da23b7e0bfe9f2c18ab6bc369c9d

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

Path: tests/wf/mut.cwl

Branch/Commit ID: aec33fcfa3459a90cbba8c88ebb991be94d21429