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

Functions

axion.elec2well Man page
axion.elec.name.to.xy Man page
axion.electrodes.on.well Man page
axion.guess.well.number Man page
axion.spikestodf Man page
axion.spikesum Man page
axion.spikesum2 Man page
burstinfo Man page
calc.burst.summary Man page
calculate.isis Man page
calculate.network.bursts Man page
calculate.network.spikes Man page
chem.info.2 Man page
construct.s Man page
filter.wells Man page
get.array.info Man page
get.data Man page
get.file.basename Man page
get.num.AE Man page
get.project.plate.name Man page
get.wt Man page
has.network.spikes Man page
IGM.aggregate.feature.data Man page
IGM.mean.firingrate.by.well Man page
IGM.plot.active.wells.network.spikes Man page
IGM.plot.distributions Man page
IGM.plot.mean.firingrate.by.eletrode.by.div Man page
IGM.plot.mean.firingrate.by.well.by.div Man page
IGM.plot.ns Man page
IGM.plot.plate.summary.for.bursts Man page
IGM.plot.plate.summary.for.spikes Man page
IGM.summary.network.spikes Man page
IGM.write.UI.to.log Man page
IGM.xyplot.network.spikes Man page
isi Man page
make.raster Man page
mi.find.bursts Man page
NB.matrix.to.feature.dfs Man page
parameters Man page
plateinfo Man page
remove.spikes Man page
S Man page
write.csv.network.spikes Man page
write.features.to.files Man page
write.pdf Man page
write.plate.summary.for.bursts Man page
write.plate.summary.for.spikes Man page

Files

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.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.