Man pages for orionzhou/rmaize
Common bioinformatic utilities
| cmp_proportion | plot proportions of a set of categories |
| cmp_proportion1 | plot proportions of a set of categories |
| complete_sample_list | complete sample list |
| desc_stat | Get summary statistics for a numeric vector |
| fit_split | fit a splited train set and validate in test set |
| flattern_gcoord | flattern 2D genome coordinates tibble[chrom, pos] to 1D... |
| flattern_gcoord_prepare | prepare flattern 2D genome coordinates |
| generate_sample_id | helper function |
| genome_dir | Get system path to genome directory |
| get_density | generate point density |
| get_grid | Get grid |
| get_model | Get default model |
| get_sra_meta | Query SRA using BioProject ID(s) and return meta table of... |
| get_tuner | Get tuner |
| go_enrich | Perform GO enrichment analysis using hypergeometric test |
| hc_order_row | use hclust to order matrix rows |
| heatmap_hc | plot a heatmap with hclust tree shown on left |
| hyper_enrich | Perform hypergeometic enrichment test on a set of genes |
| hyper_enrich_m | Perform hypergeometric enrichment test on multiple gene sets |
| idist | a unified distance function with custome methods |
| intersect_basepair | bedtools intersect |
| intersect_cds_sv | bedtools intersect |
| intersect_count | bedtools intersect |
| intersect_gene | bedtools intersect |
| intersect_idx | bedtools intersect |
| intersect_idx_maxovlp | bedtools intersect |
| intersect_idx_t | bedtools intersect |
| intersect_once | bedtools intersect |
| intersect_s | bedtools intersect |
| intersect_score | bedtools intersect |
| lg | quick linear regression |
| liftover | liftOver |
| load_fonts | Generate load custom fonts |
| load_txdb | laod txdb |
| lsos | Improved List of Objects |
| make_tile | make sliding window/tile |
| merge_reps | merge replicates |
| metric_balanced | obtian balanced metrics from truth/prediction |
| metrics6 | Default metrics set for motif prediction |
| ml0 | train a simple model using default parameters |
| ml1 | train best model using gird search and vfold-CV |
| Mode | get most frequent item in a vector |
| otheme | flexible custom ggplot theme |
| pal_10 | Generate a color palette (n=10) |
| pal_12 | Generate a color palette (n=12) |
| pal_13 | Generate a color palette (n=13) |
| pal_23 | Generate a color palette (n=23) |
| pal_23b | Generate a color palette (n=23) |
| pal_gradient | Generate a gradient color palette (n=100) |
| pal_shapes | Generate a shape palette (<=15) |
| plot_ase | plot ASE allele-frequency boxplot |
| plot_hclust | plot hclust |
| plot_hist | quick plot histogram |
| plot_pca | plot PCA |
| plot_ril_genotype | plot RIL haplotype blocks |
| plot_tsne | plot tsne |
| plot_umap | plot umap |
| readcount_norm | normalize RNA-Seq read count matrix |
| read_genome_conf | Read Genome Configuration |
| read_go | Read GO annotation for B73 AGP_v4 |
| read_gspread | read a generic googlesheet |
| read_gspread_master | read Google Spreadsheet "maize_studies" |
| read_regions | Get maize ACR |
| read_sra_run | Read SRA run table, format to tibble |
| read_symbol | Get maize gene symbols |
| read_syn | Get maize syntenic genes |
| read_tf | Read TF IDs |
| rnaseq_cpm | read one RNA-Seq study result (final) |
| rnaseq_cpm_raw | read one RNA-Seq study result (raw) |
| rnaseq_mapping_stat | get RNA-Seq mapping stats |
| rnaseq_sample_meta | get RNA-Seq sample meta table |
| set_bound | set bound to a value/vector |
| sortC | sort utility |
| sra_fill_replicate | Fill in 'Replicate' column of a sample table |
| sum_stat_tibble | Get summary statistics for the 2nd+ columns of a tibble |
| test_enrich | Generic function to perform hypergeometric/fisher exact test... |
| v3_to_v4 | Read maize v3 to v4 gene ID mapping |
