almeidasilvaf
Bioinformatics. Network biology. Plant genomics and evolution. #rstats addict.
VIB-UGent Center for Plant Systems BiologyTechnologiepark 71, Ghent, Belgium
Pinned Repositories
bears
An R package to create gene expression atlases from bulk RNA-seq data on NCBI SRA
BioNERO
Easy and comprehensive biological network reconstruction and analysis
cogeqc
An R package to perform systematic quality checks on comparative genomics analyses
CompEvoBio
Written materials for the course "Introduction to Computational Evolutionary Biology"
doubletrouble
An R package to identify and classify duplicated genes from whole-genome protein sequence data
doubletroubledb
A dashboard to explore and download the duplicated gene repertoire in eukaryote species
EuroBioc2022_synteny_networks
Material for the workshop "Inference and Analysis of Synteny Networks with syntenet", presented at EuroBioc2022
HybridExpress
An R package for comparative transcriptomic analyses of hybrids and their progenitors
SoyFungi_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"
syntenet
An R package to infer and analyze synteny networks from protein sequences
almeidasilvaf's Repositories
almeidasilvaf/BioNERO
Easy and comprehensive biological network reconstruction and analysis
almeidasilvaf/syntenet
An R package to infer and analyze synteny networks from protein sequences
almeidasilvaf/doubletrouble
An R package to identify and classify duplicated genes from whole-genome protein sequence data
almeidasilvaf/HybridExpress
An R package for comparative transcriptomic analyses of hybrids and their progenitors
almeidasilvaf/cogeqc
An R package to perform systematic quality checks on comparative genomics analyses
almeidasilvaf/doubletroubledb
A dashboard to explore and download the duplicated gene repertoire in eukaryote species
almeidasilvaf/bears
An R package to create gene expression atlases from bulk RNA-seq data on NCBI SRA
almeidasilvaf/CompEvoBio
Written materials for the course "Introduction to Computational Evolutionary Biology"
almeidasilvaf/almeidasilvaf.github.io
Personal website and blog
almeidasilvaf/cageminer
Candidate Gene Miner
almeidasilvaf/cogeqc_paper
Data and code associated with the paper "Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package"
almeidasilvaf/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/HybridExpress_paper
Data and code associated with the paper "HybridExpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors"
almeidasilvaf/magrene
Motif analysis in gene regulatory networks
almeidasilvaf/polyploid_GRNs
Code and data associated with the manuscript "Whole-genome duplications and the long-term evolution of gene regulatory networks in angiosperms"
almeidasilvaf/rnaseq_intro
Code handouts for the course "Introduction to RNA-seq analysis with R/Bioconductor"
almeidasilvaf/SEA_paper
Code and data associated with the paper 'The Soybean Expression Atlas v2: a comprehensive database of over 5000 RNA-seq samples'
almeidasilvaf/SoybeanAtlas_issues
A repo to report issues on the Soybean Expression Atlas database.
almeidasilvaf/planttfhunter
An R package to identify plant transcription factors from protein sequence data and classify them in families
almeidasilvaf/bioc-rnaseq
Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor
almeidasilvaf/blogcomments
Repo to store comments in my blog posts
almeidasilvaf/exdiva
An R package to compute expression divergence metrics
almeidasilvaf/NAR
Materials for the course "Network Analysis in R"
almeidasilvaf/NASB
Materials for the course "Network Analysis in Systems Biology with R/Bioconductor"
almeidasilvaf/PCMR_solutions
Solutions for the practice problems in the book "Phylogenetic Comparative Methods in R", by Liam Revell and Luke Harmon
almeidasilvaf/pkg_status
A repo to track the build status of my R packages on Bioconductor and GitHub
almeidasilvaf/presentations
Slide presentations for talks I've given
almeidasilvaf/r-bioc-intro
Materials for the course "Introduction to R/Bioconductor"
almeidasilvaf/SoyPestGCN_paper
Data and code associated the the SoyPestGCN paper
almeidasilvaf/tidyproj
An R package to create a standard project structure for reproducible research