Man pages for TYMichaelsen/mmtravis
Tools for analysing (meta)transcriptomics data
| grapes-w-slash-o-grapes | x without y |
| mt_batch | Correct for batch-effects in 'mmt' objects based on... |
| mt_diffexprs | Calculate differential expression statistics by a grouping... |
| mt_dumpDE | Extract results from DE analysis done using 'mt_diffexprs'. |
| mt_enrichCOG | Perform enrichment analysis using COG categories. |
| mt_enrichKO | Perform enrichment analysis using KEGG annotation. |
| mt_gather | Gather the mmt object into one dataframe, suitable for e.g.... |
| mt_GenomeFrequencyMatrix | Computes a by-genome frequency matrix of any attribute in the... |
| mt_load | Load the transcriptomics data, associated gene data and... |
| mt_loadMetaT | Load data produced by the MetaT pipeline into R. |
| mt_phi | Calculates the phi-statistic of all genes in 'mmt' object. |
| mt_plotpairs | Plot multiple combinations of sample gene expressions in a... |
| mt_stackbar | Make a stacked barplot of the sequencing statistics. |
| mt_subset | Normalise and subset the data in 'mmt' objects based on... |
| print.mmt | Prints mmt object summary (internal function) |
| setroworder | The row-version of setcolorder in data.table (internal... |
| test_pathway | performs a hypergeometric test on a set of genes (internal... |
| vis_boxplot | Visually appealing boxplots |
| vis_ordinate | Visually appealing ordination plots |
