An R Package for Time Course RNASeq Data Analysis

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Documentation for package ‘moanin’ version 1.16.1

• 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