Explore Workflows

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

Path: definitions/subworkflows/molecular_alignment.cwl

Branch/Commit ID: f401b02285f30de1c12ac2859134099fe04be33f

Accept and archive simulation model parameter(s). Acceptances includes review of validation process.

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

Path: workflows/AcceptParameter.cwl

Branch/Commit ID: 13a1a949db93afa18ffe8180ff9549e395184e4b

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

Path: tests/wf/mut.cwl

Branch/Commit ID: 9f3b9e7b74d5a904b12674dfd1300b56a48c3d33

Workflow to run the TMB analysis on a batch of samples and merge the results back into a single data clinical file

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

Path: cwl/tmb_workflow.cwl

Branch/Commit ID: 462f6015c9268a4205b6e81de018a470b8a4a153

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

Path: cwltool/schemas/v1.0/v1.0/count-lines5-wf.cwl

Branch/Commit ID: 8010fd2bf1e7090ba6df6ca8c84bbb96e2272d32

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

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom2-wf.cwl

Branch/Commit ID: 2ae8117360a3cd4909d9d3f2b35c30bfffb25d0a

Differential gene expression analysis ===================================== Differential gene expression analysis based on the negative binomial distribution Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. DESeq1 ------ High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. Simon Anders and Wolfgang Huber propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, [DESeq](http://bioconductor.org/packages/release/bioc/html/DESeq.html), as an R/Bioconductor package DESeq2 ------ In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. [DESeq2](http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html), a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.

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

Path: workflows/deseq.cwl

Branch/Commit ID: 44214a9d02e6d85b03eb708552ed812ae3d4a733

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

Path: definitions/subworkflows/filter_vcf_nonhuman.cwl

Branch/Commit ID: 4aba7c6591c2f1ebd827a36d325a58738c429bea

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

Path: definitions/pipelines/detect_variants_wgs.cwl

Branch/Commit ID: 9143dc4ebacb9e1df36a712b0be6fa5d982b0c4f

Generate ATDP heatmap centered on TSS from an array of input BAM files and genelist TSV file. Returns array of heatmap JSON files with the names that have the same basenames as input BAM files, but with .json extension

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

Path: workflows/heatmap.cwl

Branch/Commit ID: 9ee330737f4603e4e959ffe786fbb2046db70a00