IGM.MEA: IGM MEA Analysis

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

Install the latest version of this package by entering the following in R:
install.packages("IGM.MEA")
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

View on CRAN

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

calc.burst.distributions Man page
calc.burst.summary Man page
calculate.burst.features Man page
calculate.isis Man page
calculate.network.bursts Man page
calculate.network.spikes Man page
calculate.spike.features Man page
dist.perm Man page
filter.wells Man page
generate.raster.plot Man page
get.burst.info Man page
get.data Man page
get.experimental.log.file 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.features Man page
IGM.compute.mean.firingrate.by.well Man page
IGM.plot.active.wells.network.spikes Man page
IGM.plot.mean.firingrate.by.eletrode.by.div Man page
IGM.plot.mean.firingrate.by.well.by.div Man page
IGM.plot.network.spikes Man page
IGM.plot.plate.summary.for.bursts Man page
IGM.plot.plate.summary.for.spikes Man page
IGM.write.UI.to.log Man page
IGM.xyplot.network.spikes Man page
isi Man page
load.spikelist Man page
mi.find.bursts Man page
NB.matrix.to.feature.dfs Man page
parameters Man page
permute.features.and.plot Man page
read.spikelist Man page
remove.spikes Man page
S Man page
si.find.bursts Man page
summarize.network.spikes Man page
write.features.to.files Man page
write.network.spikes.to.csv Man page
write.plate.summary.for.bursts Man page
write.plate.summary.for.spikes Man page

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

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.