An R Package for Time Course RNASeq Data Analysis

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Documentation for package ‘moanin’ version 1.8.0

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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