IGM.MEA: IGM MEA Analysis
Version 0.3.5

Software tools for the characterization of neuronal networks as recorded on multi-electrode arrays.

AuthorQuanli Wang, Sahar Gelfman, Diana Hall, Ryan Dhindsa
Date of publication2017-03-05 08:47:12
MaintainerSahar Gelfman <sg3261@columbia.edu>
LicenseGPL (>= 3)
Version0.3.5
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("IGM.MEA")

Getting started

IGM.MEA: Performing a Comprehensive Analysis of Multiple MEA Recordings

Popular man pages

calc.burst.distributions: calculate and plot burst featues distributions
calculate.network.bursts: Compute network bursts for a list of MEA recordings.
get.burst.info: get burst feature information
IGM.aggregate.features: Aggregate Feature Data
IGM.write.UI.to.log: IGM.write.UI.to.log
load.spikelist: Load Robject File
read.spikelist: Axion convert spkList to Robject
See all...

All man pages Function index File listing

Man pages

caclulate.burst.features: Filter spikes and bursts in recording objects
caclulate.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...
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.
dist.perm: Burst distribution permutations
filter.wells: Filter wells
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.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.features: Aggregate Feature Data
IGM.compute.mean.firingrate.by.well: mean.firingrate.by.well
IGM.plot.active.wells.network.spikes: plot.active.wells.network.spikes
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.network.spikes: 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.write.UI.to.log: IGM.write.UI.to.log
IGM.xyplot.network.spikes: xyplot for network spikes at the plate level.
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...
permute.features.and.plot: Write PDF
read.spikelist: Axion convert spkList to Robject
remove.spikes: remove.spikes
S: example 'S' object
si.find.bursts: Find bursts
summarize.network.spikes: Generate network spikes based features.
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

Functions

IGM.aggregate.features Man page Source code
IGM.compute.mean.firingrate.by.well Man page Source code
IGM.plot.active.wells.network.spikes Man page Source code
IGM.plot.mean.firingrate.by.eletrode.by.div Man page Source code
IGM.plot.mean.firingrate.by.well.by.div Man page Source code
IGM.plot.network.spikes Man page Source code
IGM.plot.plate.summary.for.bursts Man page Source code
IGM.plot.plate.summary.for.spikes Man page Source code
IGM.write.UI.to.log Man page Source code
IGM.xyplot.network.spikes Man page Source code
NB.Extract.Features Source code
NB.Gaussian.Filter Source code
NB.Get.Burst.Stats.Intensities Source code
NB.Get.Spike.Stats Source code
NB.Merge.Result Source code
NB.matrix.to.feature.dfs Man page Source code
NB.prepare Source code
NB.select.and.bin Source code
Robject.read.spikes Source code
S Man page
active.wells.network.spikes Source code
apply.perm.and.plot Source code
as.data.frame.network.spikes Source code
axion.elec.name.to.xy Source code
axion.elec2well Source code
axion.electrodes.on.well Source code
axion.guess.well.number Source code
axion.spikestodf Source code
axion.spikesum2 Source code
bin.distances Source code
calc.all.ibi Source code
calc.all.isi Source code
calc.burst.distributions Man page Source code
calc.burst.summary Man page Source code
calc.ibi Source code
calculate.burst.features Man page Source code
calculate.isis Man page Source code
calculate.network.bursts Man page Source code
calculate.network.spikes Man page Source code
calculate.spike.features Man page Source code
channel.plot.by.well Source code
check.spikes.monotonic Source code
compile.ns Source code
compute.ns Source code
construct.s Source code
corr.do.fit Source code
corr.get.means Source code
corr.index Source code
create.feat.df Source code
dist.perm Man page Source code
extract.rows Source code
filter.channel.names Source code
filter.spikes.Robject Source code
filter.wells Man page Source code
find.halfmax Source code
find.peaks Source code
generate.raster.plot Man page Source code
get.all.electrodes Source code
get.array.info Source code
get.burst.info Man page Source code
get.burst.info.averaged.over.well Source code
get.data Man page Source code
get.div Source code
get.electrode.layout Source code
get.experimental.log.file Man page Source code
get.file.basename Man page Source code
get.num.AE Man page Source code
get.project.plate.name Man page Source code
get.wt Man page Source code
graythresh Source code
has.network.spikes Man page Source code
isi Man page Source code
load.spikelist Man page Source code
locpeaks Source code
logisi.compute Source code
logisi.find.burst Source code
make.corr.indexes2 Source code
make.distances Source code
make.spikes.to.frate Source code
mann.whit.perm Source code
mean.burst.summary Source code
mean.ns Source code
mi.find.bursts Man page Source code
my.upper Source code
names.to.indexes Source code
num.bursts Source code
parameters Man page
permute.features.and.plot Man page Source code
plateinfo Source code
plot.burst.info Source code
plot.feature Source code
plot.isis.by.electrode Source code
plot.isis.by.plate Source code
plot.mealayout Source code
plot.mean.firingrate.by.electrode Source code
plot.meanfiringrate Source code
plot.spike.list Source code
print.spike.list Source code
read.spikelist Man page Source code
remove.spikes Man page Source code
si.find.burst2 Source code
si.find.bursts Man page Source code
sort.df Source code
spike.simulation Source code
spike.summary.by.electrode Source code
spike.summary.by.well Source code
spikes.to.bursts Source code
spikes.to.count2 Source code
spkList.to.Robject Source code
spkList2list Source code
summarize.network.spikes Man page Source code
summary.ns Source code
summary.spike.list Source code
surprise Source code
tiling.allpairwise Source code
trim.trailing Source code
wilcox.test.perm Source code
write.burst.summary Source code
write.features.to.files Man page Source code
write.network.spike.summary Source code
write.network.spikes.to.csv Man page Source code
write.plate.summary.for.bursts Man page Source code
write.plate.summary.for.spikes Man page Source code
write.spike.summary Source code

Files

inst
inst/extdata
inst/extdata/exampleRecording_1012016_plate1_DIV4_spike_list.csv.gz
inst/extdata/exampleRecording_1012016_plate1_DIV1_spike_list.csv.gz
inst/extdata/exampleRecording_1012016_plate1_expLog.csv.gz
inst/extdata/exampleRecording_1012016_plate1_DIV3_spike_list.csv.gz
inst/doc
inst/doc/IGM.MEAgeneralUsage.Rmd
inst/doc/IGM.MEAgeneralUsage.R
inst/doc/IGM.MEAgeneralUsage.html
src
src/sjemea.c
src/registerC.c
src/tiling.c
NAMESPACE
data
data/S.RData
data/parameters.r
R
R/bursts.R
R/utils.R
R/make.raster.R
R/axion.R
R/logisi.R
R/corrIndex.R
R/MEA_functions.R
R/aggregateData.R
R/permPlot.R
R/burstDistributions_functions.R
R/networkspikes.R
R/si.R
R/burst_stats.R
R/maxinterval.R
R/NetworkBurst_functions.R
R/networkspikes_functions.R
R/spikes.R
R/zzz.R
R/spikelist_functions.R
vignettes
vignettes/IGM.MEAgeneralUsage.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/filter.wells.Rd
man/si.find.bursts.Rd
man/get.file.basename.Rd
man/get.data.Rd
man/IGM.plot.plate.summary.for.spikes.Rd
man/IGM.aggregate.features.Rd
man/caclulate.burst.features.Rd
man/load.spikelist.Rd
man/IGM.write.UI.to.log.Rd
man/write.network.spikes.to.csv.Rd
man/calculate.network.spikes.Rd
man/mi.find.bursts.Rd
man/dist.perm.Rd
man/get.burst.info.Rd
man/get.project.plate.name.Rd
man/generate.raster.plot.Rd
man/IGM.plot.plate.summary.for.bursts.Rd
man/calculate.isis.Rd
man/has.network.spikes.Rd
man/NB.matrix.to.feature.dfs.Rd
man/IGM.plot.mean.firingrate.by.eletrode.by.div.Rd
man/IGM.plot.mean.firingrate.by.well.by.div.Rd
man/isi.Rd
man/permute.features.and.plot.Rd
man/get.experimental.log.file.Rd
man/write.plate.summary.for.bursts.Rd
man/write.features.to.files.Rd
man/get.wt.Rd
man/caclulate.spike.features.Rd
man/IGM.plot.active.wells.network.spikes.Rd
man/calc.burst.summary.Rd
man/parameters.Rd
man/S.Rd
man/IGM.xyplot.network.spikes.Rd
man/summarize.network.spikes.Rd
man/read.spikelist.Rd
man/IGM.compute.mean.firingrate.by.well.Rd
man/IGM.plot.network.spikes.Rd
man/remove.spikes.Rd
man/write.plate.summary.for.spikes.Rd
man/get.num.AE.Rd
man/calc.burst.distributions.Rd
man/calculate.network.bursts.Rd
IGM.MEA documentation built on May 19, 2017, 9:49 p.m.

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