Workflows
What is a Workflow?Filters
The simplest workflow among a collection of workflows intended to solve tasks up to CTF estimation.
Type: Nextflow
Creators: Arnau Soler Costa, Amy Curwin, Jordi Rambla, All the Sarek team, nf-core comunity and people in the IMPaCT-Data project.
Submitter: Arnau Soler Costa
Type: Nextflow
Creators: Usman Rashid, Chen Wu, Jason Shiller, Ken Smith, Ross Crowhurst, Marcus Davy, Ting-Hsuan Chen, Susan Thomson, Cecilia Deng
Submitter: Usman Rashid
Workflow for gene set enrichment analsysis (GSEA) and co-expression analysis (WGCNA) on transcriptomics data to analyze pathways affected in Porto-Sinusoidal Vascular Disease.
Type: Common Workflow Language
Creators: Aishwarya Iyer, Friederike Ehrhart
Submitter: Aishwarya Iyer
Predict variants and drug resistance from M. tuberculosis sequence samples (Illumina)
Variant Interpretation Pipeline (VIP) that annotates, filters and reports prioritized causal variants in humans, see https://github.com/molgenis/vip for more information.
pod5_by_pore
A Snakemake workflow to take the POD5 files produced by an Oxford Nanopore sequencing run and re-batch them by pore (ie. by channel).
This is useful if you want to run duplex basecalling because you can meaningfully run "dorado duplex" on a single (or a subset of) the POD5 files.
Know issues
It is assumed all POD5 input files are from the same sequencing run, but this is not checked.
beacon-omop-worker-workflows
GBMatch_CNN
Work in progress... Predicting TS & risk from glioblastoma whole slide images
Reference
Upcoming paper: stay tuned...
Dependencies
python 3.7.7
randaugment by Khrystyna Faryna: https://github.com/tovaroe/pathology-he-auto-augment
tensorflow 2.1.0
scikit-survival 0.13.1
pandas 1.0.3
lifelines 0.25.0
Description
The pipeline implemented here predicts transcriptional subtypes and survival of glioblastoma patients based on H&E stained whole slide scans. Sample data is ...