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