Package: topdownr 1.27.0

Sebastian Gibb

topdownr: Investigation of Fragmentation Conditions in Top-Down Proteomics

The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.

Authors:Sebastian Gibb [aut, cre], Pavel Shliaha [aut], Ole Nørregaard Jensen [aut]

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topdownr.pdf |topdownr.html✨
topdownr/json (API)
NEWS

# Install 'topdownr' in R:

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

Bug tracker:https://github.com/sgibb/topdownr/issues

Datasets:

tds - TopDownSet Example Data

On BioConductor:topdownr-1.27.0(bioc 3.20)topdownr-1.26.0(bioc 3.19)

bioconductor-package

33 exports 1.00 score 128 dependencies

Last updated 2 months agofrom:f5a82bf9e3

Exports:aggregate assayData bestConditions colData colData<-combine conditionData conditionData<-conditionNames createExperimentsFragmentOptimisation createTngFusionMethFiles expandMs1Conditions expandTms2Conditions filterCv filterInjectionTime filterIntensity filterNonReplicatedFragments fragmentationMap FragmentViews mz normalize readTopDownFiles removeEmptyConditions rowViews runScanHeadsman runXmlMethodChanger show summary updateConditionNames updateMedianInjectionTime validMs1Settings validTms2Settings writeMethodXmls

Dependencies:abind affy affyio AnnotationFilter askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocManager BiocParallel Biostrings bslib cachem cli clue cluster codetools colorspace cpp11 crayon crosstalk curl data.table DelayedArray digest doParallel dplyr evaluate fansi farver fastmap fontawesome foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable highr htmltools htmlwidgets httr igraph impute IRanges isoband iterators jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle limma magrittr MALDIquant MASS Matrix MatrixGenerics matrixStats memoise mgcv mime MsCoreUtils MSnbase MultiAssayExperiment munsell mzID mzR ncdf4 nlme openssl pcaMethods pillar pkgconfig plotly plyr preprocessCore promises ProtGenerics PSMatch purrr QFeatures R6 rappdirs RColorBrewer Rcpp reshape2 Rhdf5lib rlang rmarkdown S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite vsn withr xfun XML XVector yaml zlibbioc

Data Generation for topdownr

Pavel V. Shliaha, Sebastian Gibb, Ole Nørregaard Jensen

Rendered fromdata-generation.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2018-12-07
Started: 2017-08-01

Fragmentation Analysis with topdownr

Pavel V. Shliaha, Sebastian Gibb, Ole Nørregaard Jensen

Rendered fromanalysis.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2019-11-22
Started: 2017-08-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Investigation of Fragmentation Conditions in Top-Down Proteomics	topdownr-package topdownr
The AbstractTopDownSet class	$,AbstractTopDownSet-method $<-,AbstractTopDownSet-method AbstractTopDownSet-class assayData,AbstractTopDownSet-method colData colData,AbstractTopDownSet-method colData<- colData<-,AbstractTopDownSet-method combine combine,AbstractTopDownSet,AbstractTopDownSet-method conditionData conditionData,AbstractTopDownSet-method conditionData<- conditionData<-,AbstractTopDownSet-method conditionNames conditionNames,AbstractTopDownSet-method dim,AbstractTopDownSet-method dimnames,AbstractTopDownSet-method removeEmptyConditions removeEmptyConditions,AbstractTopDownSet-method rowViews rowViews,AbstractTopDownSet-method show,AbstractTopDownSet-method summary,AbstractTopDownSet-method updateConditionNames updateConditionNames,AbstractTopDownSet-method updateMedianInjectionTime updateMedianInjectionTime,AbstractTopDownSet-method updateMedianInjectionTime,TopDownSet-method [,AbstractTopDownSet,ANY,ANY,ANY-method [[,AbstractTopDownSet,ANY,missing,-method [[,AbstractTopDownSet,ANY,missing-method [[<-,AbstractTopDownSet,ANY,missing,-method [[<-,AbstractTopDownSet,ANY,missing-method
Create fragment optimisation experiment	createExperimentsFragmentOptimisation
Windows specific functions.	createTngFusionMethFiles runScanHeadsman runXmlMethodChanger
Expand MS Conditions	expandMs1Conditions expandTms2Conditions
The FragmentViews class	coerce,FragmentViews,data.frame-method combine,FragmentViews,FragmentViews-method combine,FragmentViews-method FragmentViews FragmentViews-class mz,FragmentViews-method show,FragmentViews-method
The NCBSet class	bestConditions bestConditions,NCBSet-method fragmentationMap fragmentationMap,NCBSet-method NCBSet-class show,NCBSet-method summary,NCBSet-method
Read top-down files.	readTopDownFiles
TopDownSet Example Data	tds
Deprecated functions in topdownr	topdownr-deprecated
The TopDownSet class	aggregate,TopDownSet-method coerce,TopDownSet,MSnSet-method coerce,TopDownSet,NCBSet-method combine,TopDownSet,TopDownSet-method filterCv filterCv,TopDownSet-method filterInjectionTime filterInjectionTime,TopDownSet-method filterIntensity filterIntensity,TopDownSet-method filterNonReplicatedFragments filterNonReplicatedFragments,TopDownSet-method normalize,TopDownSet-method plot,TopDownSet,missing-method show,TopDownSet-method summary,TopDownSet-method TopDownSet-class
List valid MS settings.	validMs1Settings validTms2Settings
Create Orbitrap Fusion Lumos method.xml files.	writeMethodXmls