Package: scbursts 1.6

Blair Drummond

scbursts: Single Channel Bursts Analysis

Provides tools to import and export from several existing pieces of ion-channel analysis software such as 'TAC', 'QUB', 'SCAN', and 'Clampfit', implements procedures such as dwell-time correction and defining bursts with a critical time, and provides tools for analysis of bursts, such as tools for sorting and plotting.

Authors:Blair Drummomd [aut], Mathieu Dextraze [ctb]

scbursts_1.6.tar.gz
scbursts_1.6.tar.gz(r-4.7-any)scbursts_1.6.tar.gz(r-4.6-any)
scbursts_1.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
scbursts/json (API)

# Install 'scbursts' in R:

install.packages('scbursts', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.64 score 44 scripts 229 downloads 57 exports 19 dependencies

Last updated from:317ecb8574. Checks:2 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	WARNING	144
source / vignettes	OK	155
linux-release-x86_64	WARNING	113
wasm-release	OK	105

Exports:bursts.check_subconductance bursts.conductance_states bursts.copy bursts.defined_by_tcrit bursts.get_gaps bursts.impose_deadtime bursts.modify_conductance bursts.pcloseds bursts.popens bursts.recombine bursts.remove_first_and_last bursts.select bursts.sort bursts.space_out bursts.start_times_update bursts.subconductance_as clampfit.read cplot.conductance_hist cplot.log_root_axes cplot.pclosed_ts cplot.popen_ts dwt.read dwt.write evt.extract_header evt.from_dwells evt.read evt.to_dwells evt.write hst.extract_header hst.read hst.write risetime.correct_gaussian scan.read segment.check_subconductance segment.closed_dwells segment.conductance_states segment.copy segment.count_closed segment.count_dwells segment.count_open segment.create segment.duration segment.dwells_by_conductance segment.dwells_by_conductance_range segment.impose_deadtime segment.modify_conductance segment.name segment.open_dwells segment.pclosed segment.pconductance segment.pconductance_range segment.popen segment.seg segment.start_time segment.subconductance_as segment.verify util.basename

Dependencies:cellranger cli cpp11 crayon glue hms lifecycle magrittr pillar pkgconfig prettyunits progress R6 readxl rematch rlang tibble utf8 vctrs

Single Channel Burst Analysis with scbursts

Rendered fromscbursts.Rmdusingknitr::rmarkdown

Last update: 2019-07-06
Started: 2019-02-27

Citation

Readme and manuals

Help Manual

Help page	Topics
Check if segment contains subconductive states	bursts.check_subconductance
Return a list of all the (sub)conductance states.	bursts.conductance_states
Copy a list of bursts (by value)	bursts.copy
Divide a recording into bursts defined by a critical time.	bursts.defined_by_tcrit
Get the gaps between bursts.	bursts.get_gaps
Imposes a deadtime to each segment in a burst.	bursts.impose_deadtime
Transform the conductance states according to a user-defined function of conductance level.	bursts.modify_conductance
Return pcloseds of every burst.	bursts.pcloseds
Return popens of every burst.	bursts.popens
Combine bursts into one recording (with obvious spaces between them).	bursts.recombine
Remove the first and last burst from the list.	bursts.remove_first_and_last
From a list of bursts, extract those that interest you by passing a selecting function.	bursts.select
Order a list of bursts by some function. For instance, popen.	bursts.sort
Artificially add amount of time between bursts (in absence of recording information).	bursts.space_out
(DON'T USE THIS) Fix meta-data of bursts.	bursts.start_times_update
Imposes a fixed conductance level (0 or 1) to all dwells with subconductance levels to each segment in a burst	bursts.subconductance_as
Read a .xlsx file output from clampfit	clampfit.read
Histogram of Conductance States	cplot.conductance_hist
Add log-root axes to histogram plot	cplot.log_root_axes
Plot Time Series (ts) of P(Closed).	cplot.pclosed_ts
Plot Time Series (ts) of P(Open).	cplot.popen_ts
Read a .dwt file.	dwt.read
Write a dwt file to disk. Writes DOS line endings. Dwells are in milliseconds	dwt.write
Extract header from evt file.	evt.extract_header
Converts dwell durations to absolute transition times.	evt.from_dwells
Read a .evt file to a table. Times are in seconds	evt.read
Calculate pulse lengths. Converts transition times to dwell durations.	evt.to_dwells
Write bursts to a .evt file.	evt.write
Extract header from hst file.	hst.extract_header
Read a MIL ".hst" file to a table.	hst.read
Write bursts to a log10(ms)-sqrt(Frequency) .hst file from open and closed tables.	hst.write
Undo the effect of the gaussian filter.	risetime.correct_gaussian
Read a scan results text file. scan.read returns a 1 segment list Reads in scan results and puts them in the same format as the output of dwt.read. See 'dwt', and 'segment' for more information.	scan.read
Check if segment contains subconductive states	segment.check_subconductance
Extract closed dwells.	segment.closed_dwells
Return a list of all the (sub)conductance states.	segment.conductance_states
Collapses a segment into dwells with alternating conductance levels.	segment.consecutives_to_dwells
Copy a segment	segment.copy
Extract number of closed dwells. In the case of subconductive states, a dwell is only closed if the conductance is exactly zero.	segment.count_closed
Extract number of dwells in segment.	segment.count_dwells
Extract number of open dwells. In the case of subconductive states, count the number of non-zero states.	segment.count_open
Create a "segment" object	segment.create
Get duration of a segment.	segment.duration
Extract dwells in conductance range. lower <= x <= upper	segment.dwells_by_conductance
Extract dwells in conductance range. lower <= x <= upper	segment.dwells_by_conductance_range
Imposes a deadtime to a segment by removing any dwell that is shorter than the deadtime.	segment.impose_deadtime
Transform the conductance states according to a user-defined function of conductance level.	segment.modify_conductance
Extract name from segment.	segment.name
Extract open dwells. (Any conductance greater than zero)	segment.open_dwells
Calculate empirical P(Closed) of a segment.	segment.pclosed
Calculate empirical P(Lower <= Conductance <= Upper) of a segment.	segment.pconductance
Calculate empirical P(Lower <= Conductance <= Upper) of a segment.	segment.pconductance_range
Calculate empirical P(Open) of a segment. (A state is considered open if the conductance is non-zero)	segment.popen
Extract segment number from segment.	segment.seg
Extract start_time from segment.	segment.start_time
Imposes a fixed conductance level (0 or 1) to all dwells with subconductance levels.	segment.subconductance_as
Detect misrecorded data.	segment.verify
Remove suffix and path from filename.	util.basename

Package: scbursts 1.6

scbursts: Single Channel Bursts Analysis

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)