Man pages for almeidasilvaf/cageminer
Candidate Gene Miner
| chr_length | Pepper chromosome lengths |
| gcn | Simulation of the output list from BioNERO::exp2gcn() with... |
| gene_ranges | Genomic coordinates of pepper genes |
| guides | Guide genes associated with defense and resistance to... |
| hubs | Example hub genes for the network stored in the gcn object |
| mine2 | Example output from mine_step2() |
| mine_candidates | Mine high-confidence candidate genes in a single step |
| mined_candidates | Example output from mined_candidates() |
| mine_step1 | Step 1: Get all putative candidate genes for a given sliding... |
| 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... |
| tfs | Pepper transcription factors |
