Workflows
What is a Workflow?Filters
Workflow for Single-cell ATAC-seq standard processing with SnapATAC2. This workflow takes a fragment file as input and performs the standard steps of scATAC-seq analysis: filtering, dimension reduction, embedding and visualization of marker genes with SnapATAC2. Finally, the clusters are manually annotated with the help of marker genes. In an alternative step, the fragment file can also be generated from a BAM file.
- newer Version: Updated SnapATAC2 version from 2.5.3 to 2.6.4
Name: Matrix Multiplication Contact Person: [email protected] Access Level: public License Agreement: Apache2 Platform: COMPSs
Description
Matrix multiplication is a binary operation that takes a pair of matrices and produces another matrix.
If A is an n×m matrix and B is an m×p matrix, the result AB of their multiplication is an n×p matrix defined only if the number of columns m in A is equal to the number of rows m in B. When multiplying A and B, the elements of the ...
Name: Matrix Multiplication Contact Person: [email protected] Access Level: public License Agreement: Apache2 Platform: COMPSs
Description
Matrix multiplication is a binary operation that takes a pair of matrices and produces another matrix.
If A is an n×m matrix and B is an m×p matrix, the result AB of their multiplication is an n×p matrix defined only if the number of columns m in A is equal to the number of rows m in B. When multiplying A and B, the elements of the ...
This publication corresponds to the Research Objects (RO) of the Baseline Use Case proposed in T.5.2 (WP5) in the BY-COVID project on “COVID-19 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection”.
Type: Quarto Markdown
Creators: Enrique Bernal-Delgado, Nina Van Goethem, Francisco Estupiñan-Romero, Marjan Meurisse, Javier González Galindo, Natalia Martínez-Lizaga, Santiago Royo-Sierra
Submitter: Marjan Meurisse
CoCoMiCo analyses on collections of simulated communities. Community: scatterplots and KW tests of cooperation and competition potentials, for each collection. Similarity: cooperation and competition potentials vs model similarity, defined as the Jaccard distance on sets of reactions. Added value: boxplots comparing the added value of models in communities.
Lysozyme in water full COMPSs application
Lysozyme in water full COMPSs application, using dataset_small
Lysozyme in water full COMPSs application
deepconsensus 1.2 snakemake pipeline
This snakemake-based workflow takes in a subreads.bam and results in a deepconsensus.fastq
- no methylation calls !
The metadata id of the subreads file needs to be: "m[numeric][numeric][numeric].subreads.bam"
Chunking (how many subjobs) and ccs min quality filter can be adjusted in the config.yaml
the checkpoint model for deepconsensus1.2 should be accessible like this: gsutil cp -r gs://brain-genomics-public/research/deepconsensus/models/v1.2/model_checkpoint/* ...
The second-level complexity workflow is one among a collection of workflows designed to address tasks up to CTF estimation. In addition to the functionalities provided by the layer 0 workflow, this workflow aims to enhance the quality of acquisition images using quality protocols.
Quality control protocols
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Movie max shift: automatic reject those movies whose frames move more than a given threshold.
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Tilt analysis: quality score based in the Power Spectrum Density (astigmatism and ...