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-4.5-noble)scbursts_1.6.tar.gz(r-4.4-noble)
scbursts_1.6.tgz(r-4.4-emscripten)scbursts_1.6.tgz(r-4.3-emscripten)
scbursts.pdf |scbursts.html✨
scbursts/json (API)

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

Peer review:

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

2.63 score 43 scripts 125 downloads 57 exports 20 dependencies

Last updated 5 years agofrom:317ecb8574. Checks:OK: 1 WARNING: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 02 2024
R-4.5-linuxWARNINGNov 02 2024

Exports:bursts.check_subconductancebursts.conductance_statesbursts.copybursts.defined_by_tcritbursts.get_gapsbursts.impose_deadtimebursts.modify_conductancebursts.pclosedsbursts.popensbursts.recombinebursts.remove_first_and_lastbursts.selectbursts.sortbursts.space_outbursts.start_times_updatebursts.subconductance_asclampfit.readcplot.conductance_histcplot.log_root_axescplot.pclosed_tscplot.popen_tsdwt.readdwt.writeevt.extract_headerevt.from_dwellsevt.readevt.to_dwellsevt.writehst.extract_headerhst.readhst.writerisetime.correct_gaussianscan.readsegment.check_subconductancesegment.closed_dwellssegment.conductance_statessegment.copysegment.count_closedsegment.count_dwellssegment.count_opensegment.createsegment.durationsegment.dwells_by_conductancesegment.dwells_by_conductance_rangesegment.impose_deadtimesegment.modify_conductancesegment.namesegment.open_dwellssegment.pclosedsegment.pconductancesegment.pconductance_rangesegment.popensegment.segsegment.start_timesegment.subconductance_assegment.verifyutil.basename

Dependencies:cellrangerclicpp11crayonfansigluehmslifecyclemagrittrpillarpkgconfigprettyunitsprogressR6readxlrematchrlangtibbleutf8vctrs

Single Channel Burst Analysis with scbursts

Drummond et al.

Rendered fromscbursts.Rmdusingknitr::rmarkdownon Nov 02 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Check if segment contains subconductive statesbursts.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 burstbursts.subconductance_as
Read a .xlsx file output from clampfitclampfit.read
Histogram of Conductance Statescplot.conductance_hist
Add log-root axes to histogram plotcplot.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 millisecondsdwt.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 secondsevt.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 statessegment.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 segmentsegment.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" objectsegment.create
Get duration of a segment.segment.duration
Extract dwells in conductance range. lower <= x <= uppersegment.dwells_by_conductance
Extract dwells in conductance range. lower <= x <= uppersegment.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