Explore Workflows

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: 4ffbad9ffeab15ec8af5f6f91bd352ef96d1ef77

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

Path: definitions/pipelines/cle_aml_trio.cwl

Branch/Commit ID: e2a34d2b8c406db9aed8e49e8bdcf36f51444379

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

Path: definitions/subworkflows/align_sort_markdup.cwl

Branch/Commit ID: 22fce2dbdada0c4135b6f0677f78535cf980cb07

https://github.com/anandanlk/community_based_fl.git

Path: decentralised_fl/CWL_Workflow/decentralizedFL.cwl

Branch/Commit ID: 98d1e91413a4307cd4ee888d7ef9f6ad51f4f006

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: 4ffbad9ffeab15ec8af5f6f91bd352ef96d1ef77

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: d297528e53b6c1ecb69b1ab27b8e03323b4463ad

Pairwise comparison

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: 96dbb414d287f4382e2d477fb1851aeaa5f14f2b

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

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

Path: tests/wf/revsort.cwl

Branch/Commit ID: 6d8c2a41e2c524e8d746020cc91711ecc3418a23

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

Path: testdata/scatter-wf3_v1_1.cwl

Branch/Commit ID: 1a01b0220aa6bbd76e81ceb19a892ac69d6047ec

Packed ID: main

Runs DESeq2 using LRT (Likelihood Ratio Test) ============================================= The LRT examines two models for the counts, a full model with a certain number of terms and a reduced model, in which some of the terms of the full model are removed. The test determines if the increased likelihood of the data using the extra terms in the full model is more than expected if those extra terms are truly zero. The LRT is therefore useful for testing multiple terms at once, for example testing 3 or more levels of a factor at once, or all interactions between two variables. The LRT for count data is conceptually similar to an analysis of variance (ANOVA) calculation in linear regression, except that in the case of the Negative Binomial GLM, we use an analysis of deviance (ANODEV), where the deviance captures the difference in likelihood between a full and a reduced model. When one performs a likelihood ratio test, the p values and the test statistic (the stat column) are values for the test that removes all of the variables which are present in the full design and not in the reduced design. This tests the null hypothesis that all the coefficients from these variables and levels of these factors are equal to zero. The likelihood ratio test p values therefore represent a test of all the variables and all the levels of factors which are among these variables. However, the results table only has space for one column of log fold change, so a single variable and a single comparison is shown (among the potentially multiple log fold changes which were tested in the likelihood ratio test). This indicates that the p value is for the likelihood ratio test of all the variables and all the levels, while the log fold change is a single comparison from among those variables and levels. **Technical notes** 1. At least two biological replicates are required for every compared category 2. Metadata file describes relations between compared experiments, for example ``` ,time,condition DH1,day5,WT DH2,day5,KO DH3,day7,WT DH4,day7,KO DH5,day7,KO ``` where `time, condition, day5, day7, WT, KO` should be a single words (without spaces) and `DH1, DH2, DH3, DH4, DH5` correspond to the experiment aliases set in **RNA-Seq experiments** input. 3. Design and reduced formulas should start with **~** and include categories or, optionally, their interactions from the metadata file header. See details in DESeq2 manual [here](https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions) and [here](https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#likelihood-ratio-test) 4. Contrast should be set based on your metadata file header and available categories in a form of `Factor Numerator Denominator`, where `Factor` - column name from metadata file, `Numerator` - category from metadata file to be used as numerator in fold change calculation, `Denominator` - category from metadata file to be used as denominator in fold change calculation. For example `condition WT KO`.

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

Path: workflows/deseq-lrt.cwl

Branch/Commit ID: dda6e8b5ada3f106a2b3bfcc1b151eccf9977726