Man pages for mirvie/mirmisc
Non-Modeling Helper Functions For Mirvie R Coders
| autoplot.mirvie_cohort_outliers | Plot a 'mirvie_cohort_outliers' object. |
| check_sample_descs | Check the sample descriptions data frame for an R&D... |
| collapse_tech_reps | Collapse (sum) technical replicates in a set of R&D... |
| collect_counts | Collect the count files of several samples into a single data... |
| convert_feather_dir_to_csvs | Make a directory of CSVs from a directory of feathers. |
| convert_gene_names | Convert gene names to/from Ensembl. |
| deseq_contrasts | Obtain pairwise contrasts with shrunken log2FC from a DESeq... |
| deseq_pairs | Get the 'mirmodels::deseq()' tables from pairs of conditions. |
| deseq_wide | Obtain DESeq object from raw counts wide dataframe. |
| df_fill_missing_genes | Fill missing gene columns in one data frame with those from... |
| downsample_count_vec | Downsample a vector of counts. |
| fgsea_basic | Get results from fast Gene Set Enrichment Analysis (GSEA) |
| filter_genes | Filter genes using a predicate function. |
| get_cohort_outliers | Detect the outlying samples in a cohort. |
| get_df_gene_names | Which gene names are also column names? |
| get_feather_path | Get the path to the folder containing the feather files. |
| get_gene_names | Get the names of all of the genes that we use. |
| get_htseq_paths | Get the paths to htseq/ directories for a given cohort. |
| mirmisc-package | mirmisc: Non-Modeling Helper Functions For Mirvie R Coders |
| mutate_genes | Apply the same function to all columns whose names are gene... |
| plot_cond_paired_pearson | Violin plots for within-condition gene Pearson correlation... |
| plot_down | Plot top 'n' most significantly enriched pathways in the... |
| plot_metrics_global | Plots comparisons between conditions in an experiment. |
| plot_var_mean_ratio | Plot median and other quantile values for variance-to-mean... |
| prep_gsea_input_gene_set | Prepare gene set input for 'fgsea::fgsea()'. |
| prep_gsea_input_lfc | Prep ranking metric gene input for 'fgsea::fgsea()'. |
| prep_rd_input | Join the sample descriptions and genes counts data frames... |
| reconcile_names | Match sample description sheet names to count file names. |
| reexports | Objects exported from other packages |
| repsim_gene_cond | Repeatedly simulate gene counts for cases and controls of a... |
