Laura Leroi
SEEK ID: https://workflowhub.eu/people/148
Location:
France
ORCID: Not specified
Joined: 8th Jul 2021
Expertise: Not specified
Tools: Not specified
Their tagsRelated items
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, 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, SolutionMake, GENEX, iPol, zxfenglab, Bioinformatics Unit IIS-FJD, omnibenchmark, BioX Fanatics, Li-Omics Lab, Metro Team, ZiemertLab, Song Lab, PanGIA, Holobionts Workflows, An Ideal Design for RNA-seq investigations into RPL, AMI2B Team, Institute for Hearing Technology and Acoustics (IHTA), Transcriptomics in unexplained recurrent pregnancy loss, E-MOBI / EKONOMIK MOBIL,S.R.L, Workflow Run Crate working group, datafun, BioFAIR, BH2025_Project30, NII Test Team, LIB, Galaxy and Beyond, Biodepot Spatial Proteomics Team, WEHI SODA Hub, Digital Platform, Anesthesia and Neurocritical Care Medicine, Digital Skills in Arts and Humanities, BioimageAIpub, Dalmolin Systems Biology Group, FAIRMD, KG-Microbe, BGIQD, CSB, EMRS, BioImagingUK, Bachelor Thesis Developeming an Algorithm for the Generation of Synthetic Scientific Workflows and Characterization of the generated Workflows, GenotoulBioinfo, mzlab, Liver Polyploidy Research Team, Computational Metabolomics (UoB), UiT-CANS, PathoFact2, Polyploid Spatial Transcriptomics Team, CCBR, FONDA T9 Project Team, Cen Occitanie's Geomateam, Exeter Genetics, HP-Phasing, CPSM, Bayrak Lab, Eco-Flow, oceanbase, Proj Renzo, UFZ Galaxy workflows, CEIT-Metaverse, EnChemTox, Tesla, FHAIVE - Finnish Hub for Development and Validation of Integrated Approaches, ZhuLab MII Group, Protea Glycosciences Analytical, Immunodynamics-Engel-Lab, NanoporeDB, SyBR Development, Membrane Protein-Lipid Interaction Database Pipeline, Grunwald Lab, SensorWF, Chocot test team, UNSW MWAC Structural Biology Facility, ELIXIR Norway, EMBL Hentze Group, ConesaLab, AdLab
Web page: Not specified
SeBiMER is the Bioinformatics Core Facility of IFREMER, the French National Institute for Ocean Science. SeBiMER is in charge of providing a large community of marine biologists with all the requirements (knowledge, softwares and data) to handle small and large scale bioinformatics projects, in a broad range of fields such as metabarcoding (eDNA), (meta-)transcriptomics and genomes assembly & annotaton.
Space: Independent Teams
Public web page: https://ifremer-bioinformatics.github.io/
ROR ID: Not specified
Department: Not specified
Country: France
City: Plouzané
Web page: https://wwz.ifremer.fr/en
Masking repeats in a genome using RepeatMasker
Associated Tutorial
This workflows is part of the tutorial Masking repeats with RepeatMasker, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Anthony ...
Type: Galaxy
Creators: Anthony Bretaudeau, Alexandre Cormier, Laura Leroi, Erwan Corre, Stéphanie Robin, Jonathan Kreplak
Submitters: GTN Bot, Armin Dadras
SAMBA is a FAIR scalable workflow integrating, into a unique tool, state-of-the-art bioinformatics and statistical methods to conduct reproducible eDNA analyses using Nextflow. SAMBA starts processing by verifying integrity of raw reads and metadata. Then all bioinformatics processing is done using commonly used procedure (QIIME 2 and DADA2) but adds new steps relying on dbOTU3 and microDecon to build high quality ASV count tables. Extended statistical analyses are also performed. Finally, SAMBA ...
Type: Nextflow
Creators: Cyril Noel, Alexandre Cormier, Laura Leroi, Patrick Durand, Laure Quintric
Submitter: Cyril Noel
Download
ASPICov was developed to provide a rapid, reliable and complete analysis of NGS SARS-Cov2 samples to the biologist. This broad application tool allows to process samples from either capture or amplicon strategy and Illumina or Ion Torrent technology. To ensure FAIR data analysis, this Nextflow pipeline follows nf-core guidelines and use Singularity containers.
Availability and Implementation: https://gitlab.com/vtilloy/aspicov
Citation: Valentin Tilloy, Pierre Cuzin, Laura Leroi, Emilie Guérin, ...
Type: Nextflow
Creators: Valentin Tilloy, Pierre Cuzin, Laura Leroi, Patrick Durand, Sophie Alain
Submitter: Valentin Tilloy
ORSON combine state-of-the-art tools for annotation processes within a Nextflow pipeline: sequence similarity search (PLAST, BLAST or Diamond), functional annotation retrieval (BeeDeeM) and functional prediction (InterProScan). When required, BUSCO completness evaluation and eggNOG Orthogroup annotation can be activated. While ORSON results can be analyzed through the command-line, it also offers the possibility to be compatible with BlastViewer or Blast2GO graphical tools.
Type: Nextflow
Creators: Cyril Noel, Alexandre Cormier, Patrick Durand, Laura Leroi, Pierre Cuzin
Submitter: Patrick Durand
