Package: SubCellBarCode 1.23.0

Taner Arslan

SubCellBarCode: SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome

Mass-Spectrometry based spatial proteomics have enabled the proteome-wide mapping of protein subcellular localization (Orre et al. 2019, Molecular Cell). SubCellBarCode R package robustly classifies proteins into corresponding subcellular localization.

Authors:Taner Arslan

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

# Install 'SubCellBarCode' in R:

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

Datasets:

hcc827Ctrl - HCC827 Control Cell Line
hcc827CtrlPSMCount - Minimum PSM Count in HCC827Ctrl Cell Line.
hcc827GEF - Gefitinib treated HCC827 Cell Line
hcc827GEFClass - Gefitinib treated HCC827 Cell Line Classification
hcc827GefPSMCount - Minimum PSM Count in HCC827 Gefitinib Cell Line.
hcc827exon - HCC827 Control Exon Cell Line
markerProteins - Marker Proteins Source

On BioConductor:SubCellBarCode-1.23.0(bioc 3.21)SubCellBarCode-1.22.0(bioc 3.20)

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

proteomics massspectrometry classification

3.78 score 1 scripts 159 downloads 3 mentions 21 exports 128 dependencies

Last updated 23 days agofrom:260c964f20. Checks:OK: 1 NOTE: 3 WARNING: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	WARNING	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	WARNING	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	WARNING	Oct 31 2024
R-4.3-mac	NOTE	Oct 31 2024

Exports:applyThresholdCompartment applyThresholdNeighborhood calculateCoveredProtein calRowMean candidateRelocatedProteins compareCls computeThresholdCompartment computeThresholdNeighborhood convert2symbol loadData markerQualityControl mergeCls mergeProbability plotBarcode plotMultipleProtein replacePrediction sankeyPlot sumProbability svmClassification svmExternalData tsneVisualization

Dependencies:AnnotationDbi askpass base64enc Biobase BiocGenerics Biostrings bit bit64 blob bslib cachem caret class cli clock codetools colorspace cpp11 crayon curl data.table DBI diagram digest dplyr e1071 evaluate fansi farver fastmap fontawesome foreach fs future future.apply generics GenomeInfoDb GenomeInfoDbData ggplot2 ggrepel globals glue gower gridExtra gtable hardhat highr htmltools htmlwidgets httr igraph ipred IRanges isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lattice lava lifecycle listenv lubridate magrittr MASS Matrix memoise mgcv mime ModelMetrics munsell networkD3 nlme nnet numDeriv openssl org.Hs.eg.db parallelly pillar pkgconfig plogr plyr png pROC prodlim progressr proxy purrr R6 rappdirs RColorBrewer Rcpp recipes reshape2 rlang rmarkdown rpart RSQLite Rtsne S4Vectors sass scales scatterplot3d shape SQUAREM stringi stringr survival sys tibble tidyr tidyselect timechange timeDate tinytex tzdb UCSC.utils utf8 vctrs viridisLite withr xfun XVector yaml zlibbioc

SubCellBarCode: Integrated workflow for robust classification and visualization of spatial proteome

Taner Arslan, Lukas Orre, Mattias Vesterlund, Yanbo Pan, Janne Lehtiö

Rendered fromSubCellBarCode.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2021-06-05
Started: 2019-02-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Apply thresholds to compartments	applyThresholdCompartment
Apply thresholds to neighborhood classification	applyThresholdNeighborhood
Evaluate marker protein coverage	calculateCoveredProtein
Compute the means of replicates	calRowMean
Identify candidate relocated proteins	candidateRelocatedProteins
Compare exon and gene centric classifications	compareCls
Probability threshold for compartment classification	computeThresholdCompartment
Probability threshold for neighborhood classification	computeThresholdNeighborhood
Convert identifier to gene symbol	convert2symbol
HCC827 Control Cell Line	hcc827Ctrl
Minimum PSM Count in HCC827Ctrl Cell Line.	hcc827CtrlPSMCount
HCC827 Control Exon Cell Line	hcc827exon
Gefitinib treated HCC827 Cell Line	hcc827GEF
Gefitinib treated HCC827 Cell Line Classification	hcc827GEFClass
Minimum PSM Count in HCC827 Gefitinib Cell Line.	hcc827GefPSMCount
Load the fractionated proteomics data	loadData
Marker Proteins Source	markerProteins
Evaluate the quality of the marker proteins	markerQualityControl
Merge compartment and neighborhood classification	mergeCls
Merge compartment probabilities to neighborhood probabilities	mergeProbability
Visualize the SubCellBarCode	plotBarcode
Visualization of multiple protein localizations	plotMultipleProtein
Replace compartment predictions to neighborhood predictions	replacePrediction
Sankey plot for condition-dependent protein relocalization	sankeyPlot
Sum compartment test data probabilities to neighborhood probabilities	sumProbability
Protein subcellular localization classification	svmClassification
Peptide/exon/transcript centric or PTM enriched classification	svmExternalData
Visualization of marker proteins by t-SNE map	tsneVisualization