- BioNERO::filt.seFiltered maize gene expression data from Shin et al., 2021.
- BioNERO::og.zma.osaOrthogroups between maize and rice
- BioNERO::osa.seRice gene expression data from Shin et al., 2021.
- BioNERO::zma.interproMaize Interpro annotation
- BioNERO::zma.seMaize gene expression data from Shin et al., 2021.
- BioNERO::zma.tfsMaize transcription factors
- cageminer::chr_lengthPepper chromosome lengths
- cageminer::gcnSimulation of the output list from BioNERO::exp2gcn() with pepper data
- cageminer::gene_rangesGenomic coordinates of pepper genes
- cageminer::guidesGuide genes associated with defense and resistance to oomycetes
- cageminer::hubsExample hub genes for the network stored in the gcn object
- cageminer::mine2Example output from mine_step2()
- cageminer::mined_candidatesExample output from mined_candidates()
- cageminer::pepper_seGene expression data from Kim et al., 2018.
- cageminer::snp_posCapsicum annuum SNPs associated with resistance to Phytophthora root rot.
- cageminer::tfsPepper transcription factors
- cogeqc::batch_summaryBUSCO summary output for batch mode
- cogeqc::interpro_athIntepro annotation for Arabidopsis thaliana's genes
- cogeqc::interpro_bolIntepro annotation for Brassica oleraceae's genes
- cogeqc::ogOrthogroups between Arabidopsis thaliana and Brassica oleraceae
- cogeqc::synnetSynteny network for Brassica oleraceae, B. napus, and B. rapa
- cogeqc::treeSpecies tree for model species
- doubletrouble::cds_scerevisiaeCoding sequences (CDS) of S. cerevisiae
- doubletrouble::diamond_interInterspecies DIAMOND output for yeast species
- doubletrouble::diamond_intraIntraspecies DIAMOND output for S. cerevisiae
- doubletrouble::fungi_kaksDuplicate pairs and Ka, Ks, and Ka/Ks values for fungi species
- doubletrouble::gmax_ksDuplicate pairs and Ks values for Glycine max
- doubletrouble::yeast_annotGenome annotation of the yeast species S. cerevisiae and C. glabrata
- doubletrouble::yeast_seqProtein sequences of the yeast species S. cerevisiae and C. glabrata
- HybridExpress::deg_countsData frame with frequencies (absolute and relative) of DEGs per contrast
- HybridExpress::deg_listList of differentially expressed genes for all contrasts
- HybridExpress::go_chlamyData frame with GO terms annotated to each gene of Chlamydomonas reinhardtii
- HybridExpress::se_chlamyExpression data (in counts) for 3 Chlamydomonas lines (P1, P2, and F1)
- magrene::gma_grnSample soybean GRN
- magrene::gma_paralogsSoybean (Glycine max) duplicated genes
- magrene::gma_ppiSample soybean PPI network
- magrene::nullsNull distribution of motif frequencies for vignette data set
- planttfhunter::classification_schemeData frame of TF family classification scheme
- planttfhunter::gsuProtein sequences of the algae species Galdieria sulphuraria
- planttfhunter::gsu_annotationDomain annotation for the algae species Galdieria sulphuraria The data set was created using the funcion 'annotate_pfam()' in local mode.
- planttfhunter::gsu_familiesTFs families of the algae species Galdieria sulphuraria The data set was created using the funcion 'classify_tfs()'.
- planttfhunter::tf_countsTF counts per family in 4 simulated species
- syntenet::angiosperm_phylogenyMicrosynteny-based angiosperm phylogeny.
- syntenet::annotationFiltered genome annotation for Ostreococcus sp. species
- syntenet::blast_listList of data frames containing BLAST-like tabular output
- syntenet::clustersSynteny network clusters of BUSCO genes for 25 eudicot species
- syntenet::edgesSynteny network of Ostreococcus genomes represented as an edge list
- syntenet::networkSynteny network of BUSCO genes for 25 eudicot species
- syntenet::proteomesFiltered proteomes of Ostreococcus sp. species
- syntenet::scerevisiae_annotGenome annotation of the yeast species S. cerevisiae
- syntenet::scerevisiae_diamondIntraspecies DIAMOND output for S. cerevisiae
