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VIB-UGent Center for Plant Systems Biology
- Technologiepark 71, Ghent, Belgium
- https://almeidasilvaf.github.io
- @almeidasilvaf
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NASB Public
Materials for the course "Network Analysis in Systems Biology with R/Bioconductor"
JavaScript UpdatedJun 3, 2024 -
almeidasilvaf.github.io Public
Personal website and blog
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CompEvoBio Public
Written materials for the course "Introduction to Computational Evolutionary Biology"
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doubletrouble_paper Public
Code and data associated with the paper "doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications"
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HybridExpress_paper Public
Data and code associated with the paper "HybridExpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors"
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BioNERO Public
Easy and comprehensive biological network reconstruction and analysis
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syntenet Public
An R package to infer and analyze synteny networks from protein sequences
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doubletrouble Public
An R package to identify and classify duplicated genes from whole-genome protein sequence data
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doubletroubledb Public
A dashboard to explore and download the duplicated gene repertoire in eukaryote species
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HybridExpress Public
An R package for comparative transcriptomic analyses of hybrids and their progenitors
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cogeqc Public
An R package to perform systematic quality checks on comparative genomics analyses
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tidyproj Public
An R package to create a standard project structure for reproducible research
R UpdatedDec 12, 2023 -
rnaseq_intro Public
Code handouts for the course "Introduction to RNA-seq analysis with R/Bioconductor"
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cogeqc_paper Public
Data and code associated with the paper "Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package"
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r-bioc-intro Public
Materials for the course "Introduction to R/Bioconductor"
JavaScript UpdatedOct 16, 2023 -
bioc-rnaseq Public
Forked from carpentries-incubator/bioc-rnaseqAnalysis and Interpretation of Bulk RNA-Seq Data using Bioconductor
R Other UpdatedSep 16, 2023 -
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SEA_paper Public
Code and data associated with the paper 'The Soybean Expression Atlas v2: a comprehensive database of over 5000 RNA-seq samples'
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SoybeanAtlas_issues Public
A repo to report issues on the Soybean Expression Atlas database.
1 UpdatedJun 19, 2023 -
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PCMR_solutions Public
Solutions for the practice problems in the book "Phylogenetic Comparative Methods in R", by Liam Revell and Luke Harmon
R UpdatedJun 2, 2023 -
polyploid_GRNs Public
Code and data associated with the manuscript "Whole-genome duplications and the long-term evolution of gene regulatory networks in angiosperms"
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bears Public
An R package to create gene expression atlases from bulk RNA-seq data on NCBI SRA
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planttfhunter Public
An R package to identify plant transcription factors from protein sequence data and classify them in families
transcription-factors plants rstats gene-families hidden-markov-models protein-domains functional-genomicsR UpdatedMar 14, 2023 -
magrene Public
Motif analysis in gene regulatory networks
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pkg_status Public
A repo to track the build status of my R packages on Bioconductor and GitHub
UpdatedJan 16, 2023 -
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