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syntenet
An R package to infer and analyze synteny networks from protein sequencesBioNERO
Easy and comprehensive biological network reconstruction and analysisdoubletrouble
An R package to identify and classify duplicated genes from whole-genome protein sequence dataHybridExpress
An R package for comparative transcriptomic analyses of hybrids and their progenitorscogeqc
An R package to perform systematic quality checks on comparative genomics analysesdoubletroubledb
A dashboard to explore and download the duplicated gene repertoire in eukaryote speciesbears
An R package to create gene expression atlases from bulk RNA-seq data on NCBI SRASoyFungi_GWAS_GCN
Data and code associated with the manuscript "Integration of genome-wide association studies and gene coexpression networks unveils promising soybean resistance genes against five common fungal pathogens"cogeqc_paper
Data and code associated with the paper "Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package"quarto_theme
Custom styling for my slide presentations with Quartocageminer
Candidate Gene MinerCompEvoBio
Written materials for the course "Introduction to Computational Evolutionary Biology"SoybeanAtlas_issues
A repo to report issues on the Soybean Expression Atlas database.SEA_paper
Code and data associated with the paper 'The Soybean Expression Atlas v2: a comprehensive database of over 5000 RNA-seq samples'rnaseq_intro
Code handouts for the course "Introduction to RNA-seq analysis with R/Bioconductor"magrene
Motif analysis in gene regulatory networkspolyploid_GRNs
Code and data associated with the manuscript "Whole-genome duplications and the long-term evolution of gene regulatory networks in angiosperms"doubletrouble_paper
Code and data associated with the paper "doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications"almeidasilvaf.github.io
Personal website and blogHybridExpress_paper
Data and code associated with the paper "HybridExpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors"Love Open Source and this site? Check out how you can help us