Software & Data Products
Below you can find a list of software tools and databases/web applications I have developed.
| Package | Description | Type | |
|---|---|---|---|
| AngioWGD |
|
An R package that contains a Shiny app to explore whole-genome duplication (WGD) events identified and dated in 470 angiosperm genomes. | database |
| doubletrouble |
|
An R package to to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks. | software |
| HybridExpress |
|
An R package to perform comparative transcriptomics analysis of hybrids (or allopolyploids) relative to their progenitor species. The package features functions to perform exploratory analyses of sample grouping, identify differentially expressed genes in hybrids relative to their progenitors, classify genes in expression categories (N = 12) and classes (N = 5), and perform functional analyses. We also provide users with graphical functions for the seamless creation of publication-ready figures that are commonly used in the literature. | software |
| cogeqc |
|
An R package to facilitate systematic quality checks on standard comparative genomics analyses, and to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. cogeqc also offers visualization functions to explore QC summary statistics. | software |
| SoybeanExpressionAtlas |
|
An R package that contains a Shiny app to explore and download data from the Soybean Expression Atlas, a database of >5000 bulk RNA-seq samples from different soybean tissues at several different conditions. | database |
| bears |
|
An R package with an RNA-seq pipeline to create gene expression atlases from publicly available bulk RNA-seq data in NCBI’s SRA. Users can download raw reads, preprocess them, map to a reference genome and transcriptome, and quantify the expression at the gene and transcript levels. The goal of bears is to make RNA-seq data analysis pipelines reproducible, with a framework built on state-of-the art methods and software tools, and all of that in the comfort of an R session. | software |
| planttfhunter |
|
An R package to identify plant transcription factors (TFs) from protein sequence data and classify them into families and subfamilies using the classification scheme implemented in PlantTFDB. TFs are identified using pre-built hidden Markov model profiles for DNA-binding domains. Then, auxiliary and forbidden domains are used with DNA-binding domains to classify TFs into families and subfamilies (when applicable). Currently, TFs can be classified in 58 different TF families/subfamilies. | software |
| magrene |
|
An R package for the identification and analysis of graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and bifan motifs. GRNs can be tested for motif enrichment by comparing motif frequencies to a null distribution generated from degree-preserving simulated GRNs. Motif frequencies can be analyzed in the context of gene duplications to explore the impact of small-scale and whole-genome duplications on gene regulatory networks. Finally, users can calculate interaction similarity for gene pairs based on the Sorensen-Dice similarity index. | software |
| syntenet |
|
An R package to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-based phylogeny reconstruction with maximum likelihood. | software |
| SoyPestGCN |
|
An R package that contains a Shiny app to let users explore a gene coexpression network inferred from RNA-seq data comprising soybean tissues infested with pests (i.e., insects and nematodes). | database |
| SoyFungiGCN |
|
An R package that contains a Shiny app to let users explore a gene coexpression network inferred from RNA-seq data comprising soybean tissues infected with phytopathogenic fungi. | database |
| cageminer |
|
An R package to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype using guide genes. Candidate genes can be scored and ranked to select promising targets for downstream experiments. | software |
| BioNERO |
|
An R package that aims to facilitate network analyses by integrating all standard analysis steps, including data preprocessing, inference of gene regulatory and coexpression network from expression data, functional analyses, and intra/interspecies network comparisons. | software |
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