almeidasilvaf Goto Github PK

almeidasilvaf.github.io

Personal website and blog

bears

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

bioc-rnaseq

Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor

bioc2021

Slides for the Lightning Talk at Bioc2021

bioccheck

bionero

Easy and comprehensive biological network reconstruction and analysis

blogcomments

Repo to store comments in my blog posts

cageminer

Candidate Gene Miner

cageminer_benchmark

Benchmarking cageminer efficiency

cogeqc

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

cogeqc_paper

Data and code associated with the paper "Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package"

compevobio

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

conpg2021

Slides for my CONPG presentation

course_dataviz

Slides for the course "Processing and visualizing data in the tidyverse"

doubletrouble

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

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"

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

gcn_gwas_fungi

May 2021.

gmpr1

Code and data associated with the paper "Pathogenesis-related protein 1 (PR-1) genes in soybean: genome-wide identification, structural analysis and expression profiling under multiple biotic and abiotic stresses"

hybridexpress

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

hybridexpress_paper

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

iqg

R solutions for the exercises in "Introduction to Quantitative Genetics", by DS Falconer.

magrene

Motif analysis in gene regulatory networks

msc_classes

Slides for presentations in Msc. classes

nar

Materials for the course "Network Analysis in R"

nasb

Materials for the course "Network Analysis in Systems Biology with R/Bioconductor"

pcmr_solutions

Solutions for the practice problems in the book "Phylogenetic Comparative Methods in R", by Liam Revell and Luke Harmon

pg_genomedata

Code to obtain genome data in the Plant Genomes dashboard

pg_transcriptomedata

Code to obtain transcriptome data in the Plant Genomes dashboard