almeidasilvaf/almeidasilvaf.github.io

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almeidasilvaf/almeidasilvaf.github.io

almeidasilvaf

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Personal website and blog

BioNERO

Easy and comprehensive biological network reconstruction and analysis

syntenet

An R package to infer and analyze synteny networks from protein sequences

HybridExpress

An R package for comparative transcriptomic analyses of hybrids and their progenitors

doubletrouble

An R package to identify and classify duplicated genes from whole-genome protein sequence data

cogeqc

An R package to perform systematic quality checks on comparative genomics analyses

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

bears

An R package to create gene expression atlases from bulk RNA-seq data on NCBI SRA

CompEvoBio

Written materials for the course "Introduction to Computational Evolutionary Biology"

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"

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 Quarto

cageminer

Candidate Gene Miner

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 networks

polyploid_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"

HybridExpress_paper

Data and code associated with the paper "HybridExpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors"