chr_length |
Pepper chromosome lengths |
gcn |
Simulation of the output list from BioNERO::exp2gcn() with pepper data |
gene_ranges |
Genomic coordinates of pepper genes |
guides |
Guide genes associated with defense and resistance to oomycetes |
hubs |
Example hub genes for the network stored in the gcn object |
mine2 |
Example output from mine_step2() |
mined_candidates |
Example output from mined_candidates() |
mine_candidates |
Mine high-confidence candidate genes in a single step |
mine_step1 |
Step 1: Get all putative candidate genes for a given sliding window |
mine_step2 |
Step 2: Get candidates in modules enriched in guide genes |
mine_step3 |
Step 3: Select candidates based on gene significance |
pepper_se |
Gene expression data from Kim et al., 2018. |
plot_snp_circos |
Circos plot of SNP distribution across chromosomes |
plot_snp_distribution |
Plot a barplot of SNP distribution across chromosomes |
score_genes |
Score candidate genes and select the top n genes |
simulate_windows |
Simulate number of genes for each sliding window |
snp_pos |
Capsicum annuum SNPs associated with resistance to Phytophthora root rot. |
tfs |
Pepper transcription factors |