Explore Workflows

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

Path: tests/wf/count-lines1-wf.cwl

Branch/Commit ID: 5bdb3d3dd47d8d1b3a1685220b4b6ce0f94c055e

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 PE sample 1** * previously analyzed ChIP-Seq paired-end experiment to be used as Sample 1 **ChIP-Seq PE sample 2** * previously analyzed ChIP-Seq paired-end 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-pe.cwl

Branch/Commit ID: 4a5c59829ff8b9f3c843e66e3c675dcd9c689ed5

Reverse the lines in a document, then sort those lines.

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

Path: v1.0/v1.0/revsort.cwl

Branch/Commit ID: f02557902989c749c9c2187c7045e340e2d76bfc

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

Path: definitions/subworkflows/fastq_to_bqsr.cwl

Branch/Commit ID: e56f1024306aeb427d8aae2fff715ed2e8b8f86f

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

Path: tests/wf/sec-wf-out.cwl

Branch/Commit ID: 75271e2a0887d47cca4077b60dd51ac763c09b63

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

Path: v1.0/v1.0/scatter-valuefrom-wf5.cwl

Branch/Commit ID: f02557902989c749c9c2187c7045e340e2d76bfc

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: 1750cd5cc653f058f521b6195e3bec1e7df1a086

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 97330968839983824a11ac32dff981d8ecb00955

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

Path: definitions/subworkflows/align_sort_markdup.cwl

Branch/Commit ID: 9a657bc8c462542dc7f57fba9e04dc1669f966ba

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: 1750cd5cc653f058f521b6195e3bec1e7df1a086