Package index • SplineOmics

All functions

InputControl: InputControl: A class for controlling and validating inputs

Level3Functions: Level3Functions: A class for level 3 utility functions

Level4Functions: Level4Functions: A class for level 3 utility functions

NumericBlockFinder: NumericBlockFinder: A class for finding numeric blocks in data

SplineOmics SplineOmics-package: Package Name: SplineOmics

add_dashed_lines(): Add dashed lines for treatment timepoints to a plot

add_feature_names(): Add Feature Names to Data

add_plot_to_html(): Add Plot to HTML Content

ask_user(): Prompt the user with a yes/no question

between_level(): Between Level Analysis

bind_data_with_annotation(): Bind Data with Annotation

build_cluster_hits_report(): Build Cluster Hits Report

build_create_gsea_report(): Build GSEA Report

build_create_limma_report(): Build Cluster Hits Report

build_explore_data_report(): Build Explore Data Report

build_hyperparams_screen_report(): Build Hyperparameters Screening Report

check_between_level_pattern(): Check for Between-Level Patterns in Top Tables

check_clustered_hits(): Check Clustered Genes Dataframe for Required Conditions

check_databases(): Check Valid Databases Dataframe

check_genes(): Check Valid Gene IDs

check_null_elements(): Check for NULL Elements in Arguments

check_params(): Check Params List for Required Conditions

check_splineomics_elements(): Check for Required Elements in the SplineOmics Object

clean_gene_symbols(): Clean the Gene Symbols

cluster_hits(): cluster_hits.R contains the exported package function cluster_hits and all the functions that make up the functionality of cluster_hits. cluster_hits clusters the hits of a time series omics datasets (the features that were significantly changed over the time course) with hierarchical clustering of the spline shape. Cluster Hits from Top Tables

control_inputs_create_gsea_report(): Control Inputs for GSEA Report

control_inputs_extract_data(): Control Inputs for Extracting Data

create_enrichr_zip(): Create a ZIP File for Enrichr Gene Lists

create_gsea_report_level(): Perform Gene Set Enrichment Analysis and plot it.

create_limma_report(): Create a limma report

create_p_value_histogram(): Create a p-value histogram from a limma top_table

create_progress_bar(): utils scripts contains shared functions that are used by at least two package functions of the SplineOmics package. Create Progress Bar

create_spline_params(): Create Spline Parameters

create_splineomics(): Create a SplineOmics object

create_toc(): Create Table of Contents

create_volcano_plot(): Create a Volcano Plot

dbs_to_term2genes(): Convert Database File to TERM2GENE List

define_html_styles(): Define HTML Styles

design2design_matrix(): Create Design Matrix for Splines

download_enrichr_databases(): Download Enrichr Databases

encode_df_to_base64(): Encode DataFrame to Base64 for HTML Embedding

enrichr_get_genesets(): Get Enrichr Gene Sets

ensure_clusterProfiler(): Ensure 'clusterProfiler' is installed and loaded

explore_data(): Generate Exploratory Plots

extract_data(): extract_data.R contains the exported package function extract_data. This function automatically recognises the data field in a table and returns the data matrix, that serves as input for the other functions of this package. This is for convenience only. Extract Numeric Matrix from Dataframe

flatten_spline_configs(): Flatten Spline Configurations

format_text(): Format text

gen_composite_spline_plots(): Generate Composite Spline Plots

gen_hitcomp_plots(): Generate Hit Comparison Plots

generate_and_write_html(): Generate and Write HTML Report

generate_avrg_diff_plots(): Generate Plots for Average Difference Conditions

generate_explore_plots(): Generate exploratory plots

generate_interaction_plots(): Generate Plots for Interaction of Condition and Time

generate_report_html(): utils scripts contains shared functions that are used by at least two package functions of the SplineOmics package. The level separation is only valid internally in this script, and has no connection to the script level of the respective exported functions scripts. Generate Report HTML

generate_reports(): Generate Reports

generate_reports_meta(): Generate Reports Metadata

generate_section_content(): Generate Section Content

generate_spline_comparisons(): Generate spline comparison plots for all condition pairs

generate_time_effect_plots(): Generate Plots for Time Effect

get_curve_values(): Calculate Curve Values Based on Top Table Filter

get_explore_plots_explanations(): Get Plot Explanations

get_header_section(): Get Header Section

get_level_hit_indices(): Get Hit Indices for a Specific Level

get_limma_combos_results(): Generate LIMMA Combination Results

get_spline_params_info(): Get Spline Parameters Info

hc_add(): Add Data to Hit Comparison Object

hc_barplot(): Generate Barplot for Hit Comparison Object

hc_new(): Create New Hit Comparison Object

hc_vennheatmap(): Generate Venn Heatmap

hierarchical_clustering(): Hierarchical Clustering of Curve Values

huge_table_user_prompter(): Check if any table in a list has more than 300 rows and prompt user for input.

is_not_na(): Check if Not All Values are NA

make_clustering_report(): Make Clustering Report

make_correlation_heatmaps(): Generate Correlation Heatmaps

make_density_plots(): Generate Density Plot

make_enrich_dotplot(): Make Enrich Dotplot

make_mds_plot(): Generate MDS Plot

make_pca_plot(): Generate PCA Plot with Dynamic Coloring

make_violin_box_plots(): Generate Violin Box Plot

manage_gsea_level(): Manage GSEA Analysis for a Specific Level

maybe_add_dashed_lines(): Conditionally add dashed lines for treatment timepoints

merge_annotation_all_levels_clustering(): Merge Annotation with All Top Tables

merge_top_table_with_annotation(): Merge Annotation with a Single Top Table

modify_limma_top_table(): Modify limma Top Table

normalize_curves(): Normalize Curve Values

open_template(): Open Template for Quick Setup

open_tutorial(): Interactive Tutorial for Getting Started

perform_clustering(): Perform Clustering

plot2base64(): Convert Plot to Base64

plot_all_mean_splines(): Plot All Mean Splines

plot_cluster_mean_splines(): Plot Consensus Shapes

plot_composite_splines(): Plot Composite Splines

plot_cv(): Coefficient of Variation (CV) Plot

plot_dendrogram(): Plot Dendrogram

plot_first_lag_autocorrelation(): First Lag Autocorrelation Coefficients Plot

plot_heatmap(): Plot Heatmap

plot_lag1_differences(): Lag-1 Differences Plot

plot_limma_combos_results(): Plot limma Combination Results

plot_mean_correlation_with_time(): Mean Correlation with Time Plot

plot_single_and_mean_splines(): Plot Single and Mean Splines

plot_spline_comparisons(): Create spline comparison plots for two conditions

plot_splines(): Plot Splines for Features Based on Top Table Information

prepare_gene_lists_for_enrichr(): Prepare Gene Lists for Enrichr and Return as String

prepare_plot_data(): Prepare Plot Data

preprocess_rna_seq_data(): Perform default preprocessing of raw RNA-seq counts

print(<SplineOmics>): Print function for SplineOmics objects

print_info_message(): Print Informational Message

process_combo(): Process Combination

process_combo_pair(): Process Combination Pair

process_config_column(): Process Configuration Column

process_enrichment_results(): Process Enrichment Results

process_field(): Process and Encode Data Field for Report

process_level_cluster(): Process Level Cluster

process_plots(): Process Plots

process_result(): Process GSEA Result for a Specific Level

process_top_table(): Process Top Table

process_within_level(): Process Within Level

read_section_texts(): Read and split section texts from a file

remove_batch_effect(): Remove Batch Effect

remove_batch_effect_cluster_hits(): Remove Batch Effect from Cluster Hits

remove_prefix(): Remove Prefix from String

run_gsea(): Generate a GSEA Report

run_limma_splines(): Run limma analysis with splines

screen_limma_hyperparams(): Limma Hyperparameters Screening

set_default_params(): Set Default Parameters

shorten_names(): Shorten Names

stop_call_false(): Stop with custom message without call.

store_hits(): Store Hits

truncate_row_names(): Truncate Row Names

update_splineomics(): Update a SplineOmics object

within_level(): Within level analysis