Man pages for fossbert/binilib
Carlo's little helper
| any2entrez | Convert Symbols or Ensembl gene ids to Entrez Ids |
| any2symbol | Convert Entrez or Ensembl gene ids to gene symbols |
| aREA_single | aREA for a single regulon |
| basic_rank_norm | Basic rank normalization of a gene expression matrix |
| basic_signature | basic_signature |
| brks_heatmap | Center heatmap color gradient at zero |
| collapse_multi | Collapsing many-to-one relationships for gene expression... |
| colorScale | colorScale |
| colVar | colVar |
| DEtransform | Variance stabilization transformation for RNAseq data |
| extract_features | Extract rows or columns from a matrix in order of interest |
| find_var_genes | Finding the most variable features of a matrix |
| geneLengths | Information on gene lengths. As derived from... |
| geneSets2regulon | Convert regular (one-tailed) gene sets to regulons |
| gsea1-class | The gsea1 class |
| gsea1T | This function performs one-tailed Gene Set Enrichment... |
| gsea2-class | The gsea2 class |
| gsea2ES | ES for 2 tail GSEA (Lim et al., 2009) - two character vectors |
| gsea2ES_regulon | ES for 2 tail GSEA (Lim et al., 2009) - Regulons |
| gsea2T | This function performs GSEA of two gene sets for a given... |
| gsea_null-methods | GSEA null model |
| gsea_regulon | This function performs GSEA for the negative and positive... |
| gs_ovlp | Score character vectors of genes and their overlap with... |
| homologyInfo | Human and Mouse Homology data Information on 16469 genes for... |
| homologyTable | Full homology data as provided by Jax Information on a more... |
| kaboxplot | Plot quantiles per column for a numeric matrix |
| lapply_pair | lapply function to apply functions in a pair-wise manner... |
| legend_col | Add a custom color gradient to a base R plot |
| lrcor | For two matched matrices, compute correlation (Spearman)... |
| mouse2human | Convert mouse gene symbols or entrez ids to human... |
| mypar | Quick changes to the plotting environment |
| order_heatmap | Order the columns of a heatmap within the constraints of a... |
| p2z | Convert p-values from a two tailed test to quantiles of the... |
| pick_probes | Find best probe if there are multiple per gene |
| plot_fgseaRes | Plot one-tailed GSEA on one signature for multiple gene sets |
| plot.gsea1 | Plot results from a one-tailed GSEA |
| plot.gsea2 | Plot 2-tailed enrichment results |
| plot.gsea2regulon | Plot 2-tailed enrichment results |
| plothm | Plot heatmap |
| plot_OneGs_MultSig | Plot ranks of a given gene set across several gene expression... |
| plot_OneReg_MultSig | Plot two tails of one regulon on multiple signatures |
| purIST | PurIST |
| randomize_eset | randomize_eset |
| randomize_regulon | Generate a randomized network |
| read_matrix | Tidyverse way to read in gene expression matrices |
| reexports | Objects exported from other packages |
| reg2tibble | transform a regulon object to a data frame / tibble |
| regulatorNames | Information on 6068 regulatory genes used in the... |
| replace_missings | Replace missing values (typically in a vector or matrix) |
| rescale01 | Rescale a numeric vector to range between 0 and 1 |
| res_msvip | Extract msviper results |
| rowTstat | Calculate row-wise Welch’s t-statistic |
| rowVar | rowVar |
| specific_n | For a signature matrix containing conditions/comparisons in... |
| split_violin | Split violin plot |
| stouffer_z | Stouffer integration of Z scores |
| topN_mat | For a numeric matrix containing samples or conditions in its... |
| tpm | tpm |
| vpres2regulon | Extract the top up and down regulated MR per sample |
| vpsig_limma | viperSignature and nullmodel using limma |
| write_matrix | Convenience function for writing gene expression to file |
