# Micro-Electro Array (MEA) Analysis

## Documentation for package ‘meaRtools’ version 1.0.4

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

## Help Pages

add_plateinfo | Provide information about a new MEA plate format.
aggregate_features | Aggregate Feature Data
calculate_burst_features | Filter spikes and bursts in recording objects
calculate_entropy_and_mi | Calculate Entropy and mututal information for each treatment level
calculate_isis | Calculate inter spike intervals
calculate_network_bursts | Compute network bursts for a list of MEA recordings.
calculate_network_spikes | Compute the netwrok spikes statistics from spike lists.
calculate_spike_features | Filter spikes and bursts in recording objects
calc_burst_distributions | calculate and plot burst featues distributions
calc_burst_summary | Calculate average and standard deviation of the bursting features.
compute_mean_firingrate_by_well | mean.firingrate.by.well
compute_mean_sttc_by_well | Compute the mean STTC averaged across all pairwise electrodes in well
compute_sttc_by_well | Compute the STTC across all pairwise electrodes in well
count_ns | Count number of spikes within evenly spaced time intervals(bins) from input spike trains.
dist_perm | Burst distribution permutations
filter_nonactive_spikes | Filter nonactive spikes from recordings
filter_wells | Filter wells
frate_counts | Estimate population firing rate using fixed-width time bins.
generate_raster_plot | generate_raster_plot
get_burst_info | get burst feature information
get_data | get_data
get_experimental_log_file | get_experimental_log_file
get_file_basename | get_file_basename
get_num_ae | get_num_ae
get_plateinfo | Return information about an MEA plate format
get_project_plate_name | get_project_plate_name
get_wt | Get WT
has_network_spikes | A utility function to check if network spikes are detected.
isi | isi
load_spikelist | Load Robject File
mi_find_bursts | Find bursts
nb_matrix_to_feature_dfs | Convert network burst data matrix to a list of data frames.
parameters | A list of parameters with default values that user can customize.
permute_features_and_plot | Write PDF
plateinfo | MEA plate information
plot.sttcp | Plot the STTCP
plot_active_wells_network_spikes | plot_active_wells_network_spikes
plot_mean_firingrate_by_eletrode_by_div | plot.mean.firingrate.by.eletrode.by.div
plot_mean_firingrate_by_well_by_div | plot.mean.firingrate.by.well.by.div
plot_network_spikes | Generic method for plotting network spikes.
plot_plate_summary_for_bursts | Plot burst features
plot_plate_summary_for_spikes | plot.plate.summary.for.spikes
publications | Show list of publications that have used this package
read_spikelist | Axion convert spk_list to r_object
read_spikelist_text | Construct an MEA object by importing from text files.
remove_spikes | remove_spikes
run_TMcpp | Compute STCC direct in Cpp
S | example 'S' object
si_find_bursts | Find bursts
sttc | Compute STTC for a pair of spike trains
sttcp | Compute
sttcp_ab | Compute STTC profile for two spike trains
sttc_allspikes1 | Compute STTC for all pairs of spike trains
summarize_network_spikes | Generate network spikes based features.
tiling_correlogramcpp | Compute all STTPs for a set of spike trains
tiling_correlogramcpp_index | Compute STTPs for just two spike trains, A and B
write_features_to_files | Write feature data to an output file
write_network_spikes_to_csv | Summarize and write netowrk spikes features into a csv file.
write_plate_summary_for_bursts | Prints bursting features
write_plate_summary_for_spikes | write_plate_summary_for_spikes
xyplot_network_spikes | xyplot for network spikes at the plate level.