Explore Workflows

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Graph Name Retrieved From View
workflow graph ST520114.cwl

https://github.com/Marco-Salvi/dtc51.git

Path: ST520114.cwl

Branch/Commit ID: 908abe780c8b766aea1e1e946d6063a41f494c3a
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome.cwl

Branch/Commit ID: 76a35e7d885790f30559beb31f3b58770e343afd
workflow graph xenbase-sra-to-fastq-pe.cwl

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

Path: subworkflows/xenbase-sra-to-fastq-pe.cwl

Branch/Commit ID: dda9e6e06a656b7b3fa7504156474b962fe3953c
workflow graph Detect Variants workflow for WGS pipeline

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/pipelines/detect_variants_wgs.cwl

Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d
workflow graph msi_workflow.cwl

Workflow to run the MSI analysis on a batch of samples

https://github.com/mskcc/pluto-cwl.git

Path: cwl/msi_workflow.cwl

Branch/Commit ID: 462f6015c9268a4205b6e81de018a470b8a4a153
workflow graph kmer_top_n_extract

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: be5ae41801b19ebc69a2889d8fdb39e8e2359611
workflow graph Align reference proteins plane complete workflow

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

Path: protein_alignment/wf_protein_alignment.cwl

Branch/Commit ID: 0b036c0e52935eeb413c784e14275b87d5eb028e
workflow graph exome alignment and tumor-only variant detection

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/pipelines/tumor_only_exome.cwl

Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d
workflow graph MAnorm SE - quantitative comparison of ChIP-Seq single-read data

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: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph wgs alignment and germline variant detection

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/pipelines/germline_wgs_gvcf.cwl

Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d