Explore Workflows

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Graph	Name	Retrieved From	View
	count-lines7-wf.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/count-lines7-wf.cwl Branch/Commit ID: 0e98de8f692bb7b9626ed44af835051750ac20cd
	Deprecated. AltAnalyze Build Reference Indices Deprecated. AltAnalyze Build Reference Indices	https://github.com/datirium/workflows.git Path: workflows/altanalyze-prepare-genome.cwl Branch/Commit ID: cc6fa135d04737fdde3b4414d6e214cf8c812f6e
	Single-Cell Differential Abundance Analysis Single-Cell Differential Abundance Analysis Compares the composition of cell types between two tested conditions	https://github.com/datirium/workflows.git Path: workflows/sc-rna-da-cells.cwl Branch/Commit ID: d76110e0bfc40c874f82e37cef6451d74df4f908
	wgs alignment and tumor-only variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/wgs.cwl Branch/Commit ID: 1437aed13d240fd624f78df2c7efb096c5079d73
	kfdrc_process_se_set.cwl	https://github.com/inab/kf-alignment-workflow.git Path: subworkflows/kfdrc_process_se_set.cwl Branch/Commit ID: 425c6561b6c52139190666b761cb0350cfd8ad9c
	qa_check_subwf.cwl This subworkflow will perform a QA check on the OxoG outputs. It will perform the QA check on a single tumour and it associated VCFs	https://github.com/david4096/OxoG-Dockstore-Tools.git Path: qa_check_subwf.cwl Branch/Commit ID: 6366ed398da10019b6d81a789291af6d909f28f4
	phase VCF	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/phase_vcf.cwl Branch/Commit ID: 60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2
	tt_kmer_top_n.cwl	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_top_n.cwl Branch/Commit ID: 29deae89a9898bb4dcfc27b7391b7d5067e65068
	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: 64f7fe4438898218fd83133efa25251078f5b27e
	Build Bismark indices Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.	https://github.com/datirium/workflows.git Path: workflows/bismark-index.cwl Branch/Commit ID: cc6fa135d04737fdde3b4414d6e214cf8c812f6e