Man pages for Jorisvansteenbrugge/TcT
Trait-based Comparative Transcriptomics

Add-Custom-TraitAdd Custom Trait
Calculate-Association-RulesCalculate Association Rules
Calc_Z_scoresCalculate Z scores of individual background distributions
Create_Filtered_SBS_MatrixCreate_Filtered_SBS_Matrix
Create.Rank.ColumnsAdd a ranking collumn for each sample that holds the negative...
Draw-ExpressionDraw_Expression
FilterRemove data rows that have a stdev of zero.
Get_annotation_presence_absenceCalculate which KO is present for each Bin
Get_matrix_featuresAutomatically identify features based on column names
getMetricDistGet Metric Dist
getMetricDistModuleGet Metric Dist module
Get_module_categoriesGet module categories
GetTraitAttributesGetTraitAttributes
Go-FishIdentify whether an annotation term has a certain expression...
gradient.legendCreate a gradiented legend
Identify_Significance_TraitIdentify_Significance_Trait
Identify-Trait-AttributesIdentify Trait Attributes
Individual-Random-Background-distributionsIndividual Random Background distributions
Model_ModuleModel Module
NormalizationNormalize RNAseq data
NormalizeNormalized RNAseq raw read counts
number.to.colorsConvert from numbers to colors
Pairwise-comparison-of-AnnotationsCreate an all versus all comparison for each annotation term
Plot-Background-Individual-GenesPlot_Background_Individual_Genes
Plot-Background-ModulesPlot_Background_Modules
Plot-Metric-ComparisonPlot_Metric_Comparison
Plot_Model_ModulePlot_Model_Module
Plot_Redundancy_TraitsPlot_Redundancy_Traits
Plot-Trait-AttributePlot Trait Attribute
Pre_process_inputPre-processing of RNAseq data
Prune-Trait-AttributesPrune Trait Attributes
Random.Annotated.Genes.bkgdBackground distribution of any two random genes with an...
Random-Background-distributions-of-TraitsGenerate a background distibution of composite Z scores
Random.Genes.bkgdBackground distribution of any two random genes in two random...
Random.Identical.Annotated.Genes.bkgdBackground distribution of two random random genes with the...
string.to.colorsConvert between strings to colors
Jorisvansteenbrugge/TcT documentation built on Sept. 26, 2022, 6:50 a.m.