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meaRtools

Micro-Electro Array (MEA) Analysis

Core algorithms for MEA spike train analysis, feature extraction, statistical analysis and plotting of multiple MEA recordings with multiple genotypes and treatments, published by Gelfman et al (2017) at <https://github.com/igm-team/meaRtools/>.

Functions (61)

IGM.plot.active.wells.network.spikes

plot_active_wells_network_spikes

example 'S' object

add_plateinfo

Provide information about a new MEA plate format.

aggregate_features

Aggregate Feature Data

calc_burst_distributions

calculate and plot burst featues distributions

calc_burst_summary

Calculate average and standard deviation of the bursting features.

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

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_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

si_find_bursts

Find bursts

sttc

Compute STTC for a pair of spike trains

sttc_allspikes1

Compute STTC for all pairs of spike trains

sttcp

Compute

sttcp_ab

Compute STTC profile for two 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.

meaRtools

Micro-Electro Array (MEA) Analysis

v1.0.4

GPL (>= 3)

Authors

Quanli Wang [aut, ctb], Sahar Gelfman [aut, ctb, cre], Diana Hall [aut, ctb], Ryan Dhindsa [aut, ctb], Matt Halvorsen [aut, ctb], Ellese Cotterill [aut, ctb], Tom Edinburgh [aut, ctb], Stephen J. Eglen [aut, ctb, ths]

Initial release

2018-7-1

meaRtools

Functions (61)

meaRtools

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