| avgExp | Calculate average gene expression between replicates |
| barGene | Create a bar plot of gene expression |
| barplotTopGSEA | Plot top n pathways according to given stat |
| calcGaps | Calculate optimal number of clusters |
| clusFigs | k-means clustered figures |
| clusGO | Pathway Enrichment Analysis on Clusters |
| clusRelev | Reorder clusters generated from clusFigs() and replot. |
| colPal | Colour palettes |
| combCounts | Combine two count tables |
| combGO_plot | Combine GO Results from DE analysis into one plot |
| corHeat | Sample correlation heatmap |
| count_plot | A function to make a plot of normalized counts |
| customGMT | Make custom gene sets |
| customGO | Custom GO Function |
| dPlot | Density Plot |
| enPlot | Generate enrichment plot from GSEA results |
| expCor | Expresion correlation plots of all gene expressions |
| exploreData | Explore your Data |
| filtGO | Filter a list of GO results to remove/replace tables with no... |
| fromEdgeR | Convert outputs from tools other than DESeq2 for... |
| fromLimma | Convert outputs from tools other than DESeq2 for... |
| GenerateGSEA | Create a rnk file for Gene Set Enrichment Analysis |
| geoMean | Calculate the geometric mean of a vector of numeric values |
| getSym | Convert to gene symbols |
| gmtHeat | Make a heatmap of gene expression grouped by gene sets |
| GO_Dot | Create a dot plot of GO results |
| GO_GEM | Run g:profiler enrichment analysis |
| GOgrep | Grep a key word from a GO results table and return specific... |
| GOHeat | Make a heatmap showing significance of groups of GO terms... |
| GOHeat2 | Dot heatmap for GO results |
| GO_plot | Generates GO figures |
| GOtab | Pander table of top n GO results |
| GO_Table | GO Table |
| GSEA | Gene Set Enrichment Analysis |
| GSEAclus | Create clusters of terms for Enrichment Map |
| GSEA_EM | Export GSEA results to format compatible with enrichment map... |
| gsea_gmt | Make a custom gmt from GSEA terms |
| gsva_plot | Run ssGSEA and make a plot |
| heatClus | Generate clusters from hierarchical heatmap clustering |
| heatClusRes | Add clusters to results or count matrix |
| interMA | Interactive MA Plot |
| interVP | Interactive Volcano Plot |
| listGO_Table | GO Table from list of GO results |
| loadData | Load HTSeq-count data from a sampleTable into a countMatrix... |
| loadFC | Function to load featureCounts data |
| makeTermList | Easily make a termlist for GOHeat() |
| MA_Plot | Custom MA Plot |
| mgrep | grep for multiple patterns |
| na.rm | Remove NAs |
| normToGene | Normalize gene expression to specific genes |
| PathWC | Make a Word Cloud of enriched pathway terms |
| plotClusBox | Make a boxplot grouped by gene sets or clusters |
| plotCor | Correlation Plotting Plot a correlation bewteen any two... |
| plotrnk | Plot the distribution of scores by gene rank |
| plotTime | Plot time course data |
| plotVenn | Make a Venn diagram |
| pseudoMA | Make a 'pseudo' MA plot Make a MA plot even when you have... |
| quart_group | Generate and assign quantiles Function great for making a... |
| read.gmt | Read a gmt file into R |
| readGMT | Read a gmt file into R |
| rmNA | Remove NAs |
| showPals | Show colour palettes from RColorBrewer |
| subGSEA | Subset GSEA results |
| subRes | Subset results objects using various parameters |
| vol3d | Make a 3D volcano plot combine 2 results objects into one... |
| volcanoPlot | Custom volcano Plot |
| write.gmt | Write a gene set to file in gmt format |
| writeGMT | Write a gene set to file in gmt format |
| zheat | Z-score normalized heatmap of gene expression |
| zheat_v2 | Z-score normalized heatmap of gene expression |
