# An R Package for Time Course RNASeq Data Analysis

## Documentation for package ‘moanin’ version 1.18.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

basis_matrix | Helper methods for the Moanin class
basis_matrix-method | Helper methods for the Moanin class
consensus_matrix | Compute consensus matrix from labels
create_go_term_mapping | Find enriched GO terms
create_moanin_model | Class Moanin
create_moanin_model-method | Class Moanin
create_timepoints_contrasts | Fit weekly differential expression analysis
create_timepoints_contrasts-method | Fit weekly differential expression analysis
degrees_of_freedom | Helper methods for the Moanin class
degrees_of_freedom-method | Helper methods for the Moanin class
DE_timecourse | Run spline models and test for DE of contrasts.
DE_timecourse-method | Run spline models and test for DE of contrasts.
DE_timepoints | Fit weekly differential expression analysis
DE_timepoints-method | Fit weekly differential expression analysis
discont_basis | Provides set of basis functions on either side of a time point, allowing for a discontinuity in the fitted functions
estimate_log_fold_change | Estimates log fold change
estimate_log_fold_change-method | Estimates log fold change
exampleData | Small data set for running examples
find_enriched_go_terms | Find enriched GO terms
get_auc_similarity_scores | Evaluate the consensus between sets of clusterings
get_log_data | Helper methods for the Moanin class
get_log_data-method | Helper methods for the Moanin class
group_variable | Helper methods for the Moanin class
group_variable-method | Helper methods for the Moanin class
group_variable<- | Helper methods for the Moanin class
group_variable<--method | Helper methods for the Moanin class
group_variable_name | Helper methods for the Moanin class
group_variable_name-method | Helper methods for the Moanin class
group_variable_name<- | Helper methods for the Moanin class
group_variable_name<--method | Helper methods for the Moanin class
log_transform | Helper methods for the Moanin class
log_transform-method | Helper methods for the Moanin class
Moanin | Class Moanin
Moanin-class | Class Moanin
Moanin-methods | Helper methods for the Moanin class
NULL-method | Rescales rows of data to be between 0 and 1
perWeek_barplot | Creates barplot of results of per-timepoint comparison
plot_cdf_consensus | Evaluate the consensus between sets of clusterings
plot_model_explorer | Evaluate the consensus between sets of clusterings
plot_splines_data | Plotting splines
plot_splines_data-method | Plotting splines
pvalues_fisher_method | Fisher's method to combine pvalues
rescale_values | Rescales rows of data to be between 0 and 1
rescale_values, | Rescales rows of data to be between 0 and 1
rescale_values-method | Rescales rows of data to be between 0 and 1
show | Helper methods for the Moanin class
show-method | Helper methods for the Moanin class
splines_kmeans | Performs splines clustering using K-means
splines_kmeans-method | Performs splines clustering using K-means
splines_kmeans_predict | Assign score and labels from raw data
splines_kmeans_predict-method | Assign score and labels from raw data
splines_kmeans_score_and_label | Assign score and labels from raw data
splines_kmeans_score_and_label-method | Assign score and labels from raw data
spline_formula | Helper methods for the Moanin class
spline_formula-method | Helper methods for the Moanin class
testData | Small data set for running examples
testGenesGO | Small data set for running examples
testMeta | Small data set for running examples
time_by_group_variable | Helper methods for the Moanin class
time_by_group_variable-method | Helper methods for the Moanin class
time_variable | Helper methods for the Moanin class
time_variable-method | Helper methods for the Moanin class
time_variable<- | Helper methods for the Moanin class
time_variable<--method | Helper methods for the Moanin class
time_variable_name | Helper methods for the Moanin class
time_variable_name-method | Helper methods for the Moanin class
time_variable_name<- | Helper methods for the Moanin class
time_variable_name<--method | Helper methods for the Moanin class
[-method | Helper methods for the Moanin class