Man pages for Jorisvansteenbrugge/TcT
Trait-based Comparative Transcriptomics
| Add-Custom-Trait | Add Custom Trait |
| Calculate-Association-Rules | Calculate Association Rules |
| Calc_Z_scores | Calculate Z scores of individual background distributions |
| Create_Filtered_SBS_Matrix | Create_Filtered_SBS_Matrix |
| Create.Rank.Columns | Add a ranking collumn for each sample that holds the negative... |
| Draw-Expression | Draw_Expression |
| Filter | Remove data rows that have a stdev of zero. |
| Get_annotation_presence_absence | Calculate which KO is present for each Bin |
| Get_matrix_features | Automatically identify features based on column names |
| getMetricDist | Get Metric Dist |
| getMetricDistModule | Get Metric Dist module |
| Get_module_categories | Get module categories |
| GetTraitAttributes | GetTraitAttributes |
| Go-Fish | Identify whether an annotation term has a certain expression... |
| gradient.legend | Create a gradiented legend |
| Identify_Significance_Trait | Identify_Significance_Trait |
| Identify-Trait-Attributes | Identify Trait Attributes |
| Individual-Random-Background-distributions | Individual Random Background distributions |
| Model_Module | Model Module |
| Normalization | Normalize RNAseq data |
| Normalize | Normalized RNAseq raw read counts |
| number.to.colors | Convert from numbers to colors |
| Pairwise-comparison-of-Annotations | Create an all versus all comparison for each annotation term |
| Plot-Background-Individual-Genes | Plot_Background_Individual_Genes |
| Plot-Background-Modules | Plot_Background_Modules |
| Plot-Metric-Comparison | Plot_Metric_Comparison |
| Plot_Model_Module | Plot_Model_Module |
| Plot_Redundancy_Traits | Plot_Redundancy_Traits |
| Plot-Trait-Attribute | Plot Trait Attribute |
| Pre_process_input | Pre-processing of RNAseq data |
| Prune-Trait-Attributes | Prune Trait Attributes |
| Random.Annotated.Genes.bkgd | Background distribution of any two random genes with an... |
| Random-Background-distributions-of-Traits | Generate a background distibution of composite Z scores |
| Random.Genes.bkgd | Background distribution of any two random genes in two random... |
| Random.Identical.Annotated.Genes.bkgd | Background distribution of two random random genes with the... |
| string.to.colors | Convert between strings to colors |
