Wolfgang Maier
SEEK ID: https://workflowhub.eu/people/222
Locations:
Not specified
, 
Germany
ORCID:
https://orcid.org/0000-0002-9464-6640
Joined: 16th Dec 2021
Expertise: Not specified
Tools: Not specified
Roles
Their tagsRelated items
Workflows developed as part of the EOSC4Cancer project.
Teams: EOSC4Cancer
Web page: https://eosc4cancer.eu
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network
Web page: https://galaxyproject.org/
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, virAnnot pipeline, Ay Lab, iPC: individualizedPaediatricCure, Harkany Lab, MOLGENIS, EJPRD WP13 case-studies workflows, Common Workflow Language (CWL) community, Testing, SeBiMER, IAA-CSIC, MAB - ATGC, Probabilistic graphical models, GenX, Snakemake-Workflows, ODA, IPK BIT, CO2MICS Lab, FAME, CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus, Quadram Institute Bioscience - Bioinformatics, HecatombDevelopment, Institute of Human Genetics, Testing RO Crates, Test Team, Applied Computational Biology at IEG/HMGU, INFRAFRONTIER workflows, OME, TransBioNet, OpenEBench, Bioinformatics and Biostatistics (BIO2 ) Core, VIB Bioinformatics Core, CRC Cohort, ICAN, MustafaVoh, Single Cell Unit, CO-Graph, emo-bon, TestEMBL-EBIOntology, CINECA, Toxicology community, Pitagora-Network, Workflows Australia, Medizinisches Proteom-Center, Medical Bioinformatics, AGRF BIO, EU-Openscreen, X-omics, ELIXIR Belgium, URGI, Size Inc, GA-VirReport Team, The Boucher Lab, Air Quality Prediction, pyiron, CAPSID, Edinburgh Genomics, Defragmentation TS, NBIS, Phytoplankton Analysis, Seq4AMR, Workflow registry test, Read2Map, SKM3, ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression, de.NBI Cloud, Meta-NanoSim, ILVO Plant Health, EMERGEN-BIOINFO, KircherLab, Apis-wings, BCCM_ULC, Dessimoz Lab, TRON gGmbH, GEMS at MLZ, Computational Science at HZDR, Big data in biomedicine, TRE-FX, MISTIC, Guigó lab, Statistical genetics, Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation, OLCF-WES, Bioinformatics Unit @ CRG, Bioinformatics Innovation Lab, BSC-CES, ELIXIR Proteomics, Black Ochre Data Labs, Zavolan Lab, Metabolomics-Reproducibility, Team Cardio, NGFF Tools, Bioinformatics workflows for life science, Workflows for geographic science, Pacific-deep-sea-sponges-microbiome, CSFG, SNAKE, Katdetectr, INFRAFRONTIER GmbH, PerMedCoE, Euro-BioImaging, EOSC-Life WP3 OC Team, cross RI project, ANSES-Ploufragan, SANBI Pathogen Bioinformatics, Biodata Analysis Group, DeSci Labs, Erasmus MC - Viroscience Bioinformatics, ARA-dev, Mendel Centre for Plant Genomics and Proteomics, Metagenomic tools, WorkflowEng, Polygenic Score Catalog, bpm, scNTImpute, Systems Biotechnology laboratory, Cimorgh IT solutions, MLme: Machine Learning Made Easy, Hurwitz Lab, Dioscuri TDA, Scipion CNB, System Biotechnology laboratory, yPublish - Bioinfo tools, NIH CFDE Playbook Workflow Partnership, MMV-Lab, EMBL-Bioimage Analysis Support, EBP-Nor, Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data, Bioinformatics Laboratory for Genomics and Biodiversity (LBGB), multi-analysis dFC, CholGen, RNA group, Plant Genomes Pipelines in Galaxy, Pathogen Genomic Laboratory, Chemical Data Lab, JiangLab, Pangenome database project, HP2NET - Framework for construction of phylogenetic networks on High Performance Computing (HPC) environment, Center for Open Bioimage Analysis, Generalized Open-Source Workflows for Atomistic Molecular Dynamics Simulations of Viral Helicases, Historical DNA genome skimming, QCDIS, Peter Menzel's Team, NHM Clark group, ESRF Workflow System (Ewoks), Kalbe Bioinformatics, Nextflow4Metabolomics, GBCS, CEMCOF, Jackson Laboratory NGS-Ops, Schwartz Lab, BRAIN - Biomedical Research on Adult Intracranial Neoplasms, Cancer Therapeutics and Drug Safety, Deepdefense, Mid-Ohio Regional Planning Commission, MGSSB, Institute for Human Genetics and Genomic Medicine Aachen, FengTaoSMU, EGA, Plant-Food-Research-Open, KrauthammerLab, Geo Workflows, grassland pDT, FunGIALab, CRIM - Computer Research Institute of Montréal, Medvedeva Lab, Metagenlab, FAIR-EASE, Protein-protein and protein-nucleic acid binding site prediction research, Culhane Lab, IDUN - Drug Delivery and Sensing, Edge Computing DAG Task Scheduling Research Group, Stratum corneum nanotexture feature detection using deep learning and spatial analysis: a non-invasive tool for skin barrier assessment, COPO, Taudière group, ErasmusMC Clinical Bioinformatics, interTwin, fluid flow modeling, EnrichDO, WorkflowResearch, Application Security - Test Crypt4GH solutions, RenLabBioinformatics, Yongxin's team, PiFlow, HLee_SeoGroup, UFZ - Image Data Management and Processing Workflows, Korean Bioinformaticians, Into the deep, XChem, CPM, SocialGene, Research Data Management ICE-2, ObjectRecognition, LiDAR, FONDA II C2, Astroparticle Lab, FAIRagro M4.4, Kgerring, QuackenbushLab, Virus sequencing team, SOS, BioImage Informatics and Analysis Workflows, BoostNano, simblockflow, CSSB, Research on Workflow scheduling, Research Data1, CSUbioinformatics, CDPP, Mr., ASD-HRS, data management, FAIR_thesis: Marine acoustic data, CellBinDB, DEEP Lab, University of Amsterdam, SIMEXP, nf-pediatric Team, Kasmanas, Structural Variation Analysis, fuzzyworkflow, CausalCoxMGM Team, Tufts University Center for Cellular Agriculture (TUCCA), Test, CrustyBase, Applied Computational Cancer Research, Click-qPCR, BAID Team, FabianLab, Vector informatics and genomics group, AlmondBreedingLab, Artificial Design for Intelligent Breeding, ELIXIR Biodiversity Community, GROTIA, Biomedical_LLM, WhiteSymmetry, Hämatologie Labor Kiel, pakbaba, Metagenomics Analysis, MTB Bioinformatics Workflows, RTC Bioinformatics, CMG-GUTS, EI Papatheodorou Group, Metagenomics Analysis of Microbiome, ColoPola: A polarimetric imaging dataset for colorectal cancer detection, AI in Zhou Lab, CEPLAS, LTER-Italy, Gevaert Lab, Kendall-Theisen lab pipelines, High Performance Scientific Computing Laboratory (HPSC), Ensembl Metazoa and Plants, BiRD, Q-Dawn, AMRMALDI, Systems and Synthetic Biology, EI Core Bioinformatics Group, Values Shape Community
Web page: Not specified
The goal of COVID-19-Biohackathon 2020 (COVID-19-BH20) is to develop and gather computational tools that can be useful for studying the biology of the virus and the disease.
The COVID-19 Programme in Workflow Hub aims to gather workflows for the analysis of COVID-19 molecular biology data and their metadata. In this programme, all workflows and their metadata will be curated and made interoperable, reusable and reproducible. All workflows and their metadata will be easily accessible to everyone ...
Teams: Connor Lab, GalaxyProject SARS-CoV-2, InSaFLU, nf-core viralrecon, CWL workflow SARS-CoV-2, V-Pipe, Test team
Web page: https://github.com/virtual-biohackathons/covid-19-bh20
A general team for the EOSC4Cancer project.
Space: EOSC4Cancer
Public web page: https://eosc4cancer.eu
This team and associated Galaxy workflows are maintained by the European Galaxy Team.
Space: Independent Teams
Public web page: https://usegalaxy.eu
Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures https://covid19.galaxyproject.org
Space: COVID-19 Biohackathon
Public web page: https://github.com/galaxyproject/SARS-CoV-2
Country: Not specified
City: Not specified
Web page: Not specified
COVID-19: variation analysis on ARTIC PE data
The workflow for Illumina-sequenced ampliconic data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming amplicon primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by primer-binding site mutations and, if possible, excludes reads derived from such ...
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 ...
This Galaxy workflow takes a list of tumor/normal sample pair variants in VCF 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 reports
The input VCF is expected to encode somatic status, somatic p-value and germline p-value of each variant in varscan somatic format, i.e., via SS, SPV and GPV INFO keys, respectively.
