IGM.MEA: IGM MEA Analysis

Software tools developed by the Institute for Genomic Medicine, Columbia University, for the characterization of neuronal networks as recorded on Multi-Electrode Arrays (MEAs).

AuthorQuanli Wang, Sahar Gelfman, Diana Hall, Ryan Dhindsa
Date of publication2016-11-17 18:33:51
MaintainerSahar Gelfman <sg3261@columbia.edu>
LicenseGPL (>= 3)
Version0.3.4.1

View on CRAN

Man pages

axion.elec2well: Extract well name from electrode name

axion.elec.name.to.xy: axion.elec.name.to.xy

axion.electrodes.on.well: axion.electrodes.on.well

axion.guess.well.number: axion.guess.well.number

axion.spikestodf: axion.spikestodf

axion.spikesum: axion.spikesum

axion.spikesum2: axion.spikesum2

burstinfo: get burst feature information

calc.burst.summary: Calculate average and standard deviation of the bursting...

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.

chem.info.2: chem.info.2

construct.s: construct.s

filter.wells: Filter wells

get.array.info: get.array.info

get.data: get.data

get.file.basename: get.file.basename

get.num.AE: get.num.AE

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.

IGM.aggregate.feature.data: Aggregate Feature Data

IGM.mean.firingrate.by.well: mean.firingrate.by.well

IGM.plot.active.wells.network.spikes: plot.active.wells.network.spikes

IGM.plot.distributions: calculate and plot burst featues distributions

IGM.plot.mean.firingrate.by.eletrode.by.div: plot.mean.firingrate.by.eletrode.by.div

IGM.plot.mean.firingrate.by.well.by.div: plot.mean.firingrate.by.well.by.div

IGM.plot.ns: Generic method for plotting network spikes.

IGM.plot.plate.summary.for.bursts: Plot burst features

IGM.plot.plate.summary.for.spikes: plot.plate.summary.for.spikes

IGM.summary.network.spikes: Generate network spikes based features.

IGM.write.UI.to.log: IGM.write.UI.to.log

IGM.xyplot.network.spikes: xyplot for network spikes at the plate level.

isi: isi

make.raster: make.raster

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...

plateinfo: Retrieve plate information

remove.spikes: remove.spikes

S: example 'S' object

write.csv.network.spikes: Summarize and write netowrk spikes features into a csv file.

write.features.to.files: Write feature data to an output file

write.pdf: Write PDF

write.plate.summary.for.bursts: Prints bursting features

write.plate.summary.for.spikes: write.plate.summary.for.spikes

Files in this package

IGM.MEA
IGM.MEA/inst
IGM.MEA/inst/extdata
IGM.MEA/inst/extdata/exampleRecording_1012016_plate1_DIV1_spike_list.csv.gz
IGM.MEA/inst/extdata/exampleRecording_1012016_plate1_expLog.csv.gz
IGM.MEA/src
IGM.MEA/src/sjemea.c
IGM.MEA/src/tiling.c
IGM.MEA/NAMESPACE
IGM.MEA/data
IGM.MEA/data/S.RData
IGM.MEA/data/parameters.r
IGM.MEA/R
IGM.MEA/R/calculateOtsu.R IGM.MEA/R/bursts.R IGM.MEA/R/local.corr.R IGM.MEA/R/axion_functions.R IGM.MEA/R/utils.R IGM.MEA/R/make.raster.R IGM.MEA/R/spike.simulation.R IGM.MEA/R/logisi.R IGM.MEA/R/corr_index.R IGM.MEA/R/plot.mm.s.R IGM.MEA/R/aggregate_data.R IGM.MEA/R/arrays.R IGM.MEA/R/MEA_functions.R IGM.MEA/R/general.R IGM.MEA/R/bci.R IGM.MEA/R/networkspikes.R IGM.MEA/R/surprise2.R IGM.MEA/R/findEpisodes.R IGM.MEA/R/perm_plot.R IGM.MEA/R/episode.detection.R IGM.MEA/R/maxinterval.R IGM.MEA/R/tiling.R IGM.MEA/R/burst_functions.R IGM.MEA/R/ms_funs.R IGM.MEA/R/NetworkBurst_functions.R IGM.MEA/R/networkspikes_functions.R IGM.MEA/R/spikes.R IGM.MEA/R/plotDistributions.R IGM.MEA/R/zzz.R
IGM.MEA/MD5
IGM.MEA/DESCRIPTION
IGM.MEA/man
IGM.MEA/man/filter.wells.Rd IGM.MEA/man/make.raster.Rd IGM.MEA/man/get.file.basename.Rd IGM.MEA/man/get.data.Rd IGM.MEA/man/IGM.plot.plate.summary.for.spikes.Rd IGM.MEA/man/construct.s.Rd IGM.MEA/man/axion.elec2well.Rd IGM.MEA/man/plateinfo.Rd IGM.MEA/man/IGM.write.UI.to.log.Rd IGM.MEA/man/IGM.plot.ns.Rd IGM.MEA/man/axion.electrodes.on.well.Rd IGM.MEA/man/calculate.network.spikes.Rd IGM.MEA/man/mi.find.bursts.Rd IGM.MEA/man/get.array.info.Rd IGM.MEA/man/write.csv.network.spikes.Rd IGM.MEA/man/get.project.plate.name.Rd IGM.MEA/man/axion.spikesum2.Rd IGM.MEA/man/IGM.plot.plate.summary.for.bursts.Rd IGM.MEA/man/calculate.isis.Rd IGM.MEA/man/write.pdf.Rd IGM.MEA/man/has.network.spikes.Rd IGM.MEA/man/NB.matrix.to.feature.dfs.Rd IGM.MEA/man/IGM.plot.mean.firingrate.by.eletrode.by.div.Rd IGM.MEA/man/IGM.plot.mean.firingrate.by.well.by.div.Rd IGM.MEA/man/burstinfo.Rd IGM.MEA/man/isi.Rd IGM.MEA/man/write.plate.summary.for.bursts.Rd IGM.MEA/man/write.features.to.files.Rd IGM.MEA/man/get.wt.Rd IGM.MEA/man/axion.spikestodf.Rd IGM.MEA/man/IGM.plot.distributions.Rd IGM.MEA/man/IGM.plot.active.wells.network.spikes.Rd IGM.MEA/man/IGM.mean.firingrate.by.well.Rd IGM.MEA/man/calc.burst.summary.Rd IGM.MEA/man/parameters.Rd IGM.MEA/man/IGM.aggregate.feature.data.Rd IGM.MEA/man/S.Rd IGM.MEA/man/IGM.xyplot.network.spikes.Rd IGM.MEA/man/axion.elec.name.to.xy.Rd IGM.MEA/man/axion.guess.well.number.Rd IGM.MEA/man/IGM.summary.network.spikes.Rd IGM.MEA/man/remove.spikes.Rd IGM.MEA/man/write.plate.summary.for.spikes.Rd IGM.MEA/man/axion.spikesum.Rd IGM.MEA/man/get.num.AE.Rd IGM.MEA/man/chem.info.2.Rd IGM.MEA/man/calculate.network.bursts.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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