Workflows
What is a Workflow?Filters
Run velocyto to get loom with counts of spliced and unspliced. It will extract the 'barcodes' from the bundled outputs.
Analyse Bulk RNA-Seq data in preparation for downstream Pathways analysis with MINERVA
Type: Galaxy
Creators: Iacopo Cristoferi, Helena Rasche, Clinical Bioinformatics Unit, Pathology Department, Eramus Medical Center
Submitter: Helena Rasche
This portion of the workflow produces sets of feature Counts ready for analysis by limma/etc.
Type: Galaxy
Creators: Iacopo Cristoferi, Helena Rasche, Clinical Bioinformatics Unit, Pathology Department, Eramus Medical Center
Submitter: Helena Rasche
Analyse Bulk RNA-Seq data in preparation for downstream Pathways analysis with MINERVA
MMGBSA simulation and calculation
This workflow is created as part of a tutorial listed on GTN. The workflow shows the steps in human copy number variance detection using the Contrl_FREEC tool.
Type: Galaxy
Creators: khaled Jumah, Katarzyna Kamieniecka, Wolfgang Maier, Krzysztof Poterlowicz, poterlowicz-lab
Submitter: Khaled Jum'ah
A variation of the Cancer variant annotation (hg38 VEP-based) workflow at https://doi.org/10.48546/workflowhub.workflow.607.1.
Like that other workflow it takes a list of tumor/normal sample pair variants in VCF format (see the other workflow for details about the expected format) and
- annotates them using the ENSEMBL Variant Effect Predictor and custom annotation data
- turns the annotated VCF into a MAF file for import into cBioPortal
- generates human-readable variant- and gene-centric ...
Call somatic, germline and LoH event variants from PE Illumina sequencing data obtained from matched pairs of tumor and normal tissue samples.
This workflow can be used with whole-genome and whole-exome sequencing data as input. For WES data, parts of the analysis can be restricted to the exome capture kits target regions by providing the optional "Regions of Interest" bed dataset.
The current version uses bwa-mem for read mapping and varscan somatic for variant calling and somatic status ...
Run baredSC in 1 dimension in logNorm for 1 to N gaussians and combine models.
Automated inference of stable isotope incorporation rates in proteins for functional metaproteomics
