This workshop introduces the new Ensembl Data Platform (https://beta.ensembl.org/), featuring improved visualisation, a modern interface, and access to key resources like HPRC and Darwin Tree of Life.
Abstract
The Ensembl Genome Browser has supported global genomics research for 25+ years, integrating data on genes, variants, and regulation across thousands of species. This workshop introduces the new Ensembl Data Platform (https://beta.ensembl.org/), featuring improved visualisation, a modern interface, and access to key resources like HPRC and Darwin Tree of Life. Participants will explore tools, gain hands-on experience, and learn how to apply Ensembl data in their research.
Abstract GenomicLand is a free, open-source platform for genomic prediction and genome-wide association studies. Developed in R software using Shiny, it supports diploid and polyploid datasets and integrates statistical learning, Bayesian, machine learning, and neural network methods. GenomicLand provides an accessible...
C. Azevedo, M. Nascimento, V. C. Fontes et al.· Crop Breeding and Applied Bi...· 0 citations
Xenbase is the Xenopus frog model organism knowledgebase, an online resource ( www.xenbase.org ) that hosts fully integrated and cross-referenced genomic and biological data to support Xenopus researchers worldwide. Xenbase hosts a vast variety of gene-centric content, including annotated genomes for X. laevis and X. t...
Christina James-Zorn, V. Ponferrada, A. Zorn· Methods in molecular biology· 0 citations
XpBrew, an end-to-end Python workflow that was applied to generate PanXpresso, a comprehensive collection of gene expression datasets covering the taxonomic breadth of plants, animals, fungi, bacteria and archaea is introduced.
Shakunthala Natarajan, Claudia Sterling, N. Choudhary et al.· bioRxiv· 0 citations
Meta2Data is a modular, largely automated pipeline implemented in Python and Bash for the retrieval, standardization, and processing of public microbiome sequencing data. It retrieves metadata from major public repositories, including INSDC and CNCB, using user-provided keywords or BioProject/BioSample identifiers. Ret...
Jia-Xuan Li, Anne Duplouy, Lin-Yang Sun· bioRxiv· 0 citations
Metagenome sequencing has revolutionized functional microbiome analysis across diverse ecosystems but is fraught with technical hurdles. We introduce MOSHPIT (MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking; https://moshpit.qiime2.org)-software built on the QIIME 2/rachis framework (Q2F) that i...
M. Ziemski, Liz Gehret, Anthony Simard et al.· Cell Genomics· 0 citations
FEDKEA, an enzyme annotation tool leveraging protein language models, and a user-friendly, FEDKEA-based metagenomic pipeline, MEnzMap, which encompasses the entire analysis workflow—from raw data quality control to function prediction and downstream analyses are designed.
Lei Zheng, Bowen Li, Siqi Xu et al.· Science Advances· 0 citations
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