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).

Author
Quanli Wang, Sahar Gelfman, Diana Hall, Ryan Dhindsa
Date of publication
2016-11-17 18:33:51
Maintainer
Sahar Gelfman <sg3261@columbia.edu>
License
GPL (>= 3)
Version
0.3.4.1

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