Formalizing and benchmarking open problems in single-cell genomics
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Updated
May 24, 2024 - Python
Formalizing and benchmarking open problems in single-cell genomics
A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.
Mycobacterial pipeline
AMR/VF LGT focused bacterial genomics analysis workflow
Nextflow pipeline for hyperparameter optimization of machine learning models
This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ
A Nextflow Pipeline to determine the fidelity of reverse transcriptases (RTs) and transcriptases from NGS data
Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.
A Nextflow workflow for generating the mutation profiles of SARS-CoV-2 genomes from Variants of Concern and Variants of Interest. COVID-MVP (https://github.com/cidgoh/COVID-MVP) can be used to visualize the mutations and functional annotations.
Single Cell Genome Sequencing data analysis pipeline
Configure workflow/pipeline tests using yaml files.
A Nextflow pipeline demonstrating how to train graph neural networks for gene regulatory network reconstruction using DREAM5 data.
Nexflow workflow job executor (for OpenEBench VRE installation)
A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, in a parallelised manner.
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