Package: cTRAP 1.25.0

Nuno Saraiva-Agostinho

cTRAP: Identification of candidate causal perturbations from differential gene expression data

Compare differential gene expression results with those from known cellular perturbations (such as gene knock-down, overexpression or small molecules) derived from the Connectivity Map. Such analyses allow not only to infer the molecular causes of the observed difference in gene expression but also to identify small molecules that could drive or revert specific transcriptomic alterations.

Authors:Bernardo P. de Almeida [aut], Nuno Saraiva-Agostinho [aut, cre], Nuno L. Barbosa-Morais [aut, led]

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

# Install 'cTRAP' in R:

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

Bug tracker:https://github.com/nuno-agostinho/ctrap/issues

Pkgdown:https://nuno-agostinho.github.io

Datasets:

On BioConductor:cTRAP-1.25.0(bioc 3.21)cTRAP-1.24.0(bioc 3.20)

differentialexpression geneexpression rnaseq transcriptomics pathways immunooncology genesetenrichment bioconductor bioinformatics cmap gene-expression l1000

5.08 score 5 stars 16 scripts 170 downloads 1 mentions 28 exports 150 dependencies

Last updated 2 months agofrom:b3d1df5f0d. Checks:OK: 1 NOTE: 3 ERROR: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	ERROR	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	ERROR	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	ERROR	Nov 29 2024
R-4.3-mac	NOTE	Nov 29 2024

Exports:analyseDrugSetEnrichment convertENSEMBLtoGeneSymbols convertGeneIdentifiers cTRAP downloadENCODEknockdownMetadata filterCMapMetadata getCMapConditions getCMapPerturbationTypes launchCMapDataLoader launchDiffExprLoader launchDrugSetEnrichmentAnalyser launchMetadataViewer launchResultPlotter listExpressionDrugSensitivityAssociation loadCMapData loadCMapZscores loadDrugDescriptors loadENCODEsamples loadExpressionDrugSensitivityAssociation parseCMapID performDifferentialExpression plotDrugSetEnrichment plotTargetingDrugsVSsimilarPerturbations predictTargetingDrugs prepareCMapPerturbations prepareDrugSets prepareENCODEgeneExpression rankSimilarPerturbations

Dependencies:AnnotationDbi AnnotationHub askpass assertthat backports base64enc BH binr Biobase BiocFileCache BiocGenerics BiocManager BiocParallel BiocVersion Biostrings bit bit64 blob broom bslib cachem cellranger cli codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr digest dplyr DT evaluate fansi farver fastmap fastmatch fgsea filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData ggplot2 ggrepel glue gtable highcharter highr hms htmltools htmlwidgets httpuv httr igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle limma lubridate magrittr MASS Matrix memoise mgcv mime munsell nlme openssl pbapply pillar pkgconfig plogr plyr png prettyunits progress promises purrr qs quantmod R.methodsS3 R.oo R.utils R6 RApiSerialize rappdirs RColorBrewer Rcpp RcppParallel readxl rematch reshape2 rhdf5 rhdf5filters Rhdf5lib rjson rlang rlist rmarkdown RSQLite S4Vectors sass scales shiny shinycssloaders snow sourcetools statmod stringfish stringi stringr sys tibble tidyr tidyselect timechange tinytex TTR UCSC.utils utf8 vctrs viridisLite withr xfun XML xtable xts XVector yaml zlibbioc zoo

cTRAP: identifying candidate causal perturbations from differential gene expression data

Bernardo P. de Almeida & Nuno Saraiva-Agostinho

Rendered fromcTRAP.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-03-27
Started: 2019-10-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Analyse drug set enrichment	analyseDrugSetEnrichment
Cross Tabulation and Table Creation	as.table.referenceComparison
Convert ENSEMBL gene identifiers to gene symbols	convertENSEMBLtoGeneSymbols
Convert gene identifiers	convertGeneIdentifiers
cTRAP package	cTRAP-package cTRAP
Operations on 'expressionDrugSensitivityAssociation' objects	dim.expressionDrugSensitivityAssociation dimnames.expressionDrugSensitivityAssociation [.expressionDrugSensitivityAssociation
Download metadata for ENCODE knockdown experiments	downloadENCODEknockdownMetadata
Filter CMap metadata	filterCMapMetadata
List available conditions in CMap datasets	getCMapConditions
Get CMap perturbation types	getCMapPerturbationTypes
Load CMap data via a visual interface	launchCMapDataLoader
Load differential expression data via a visual interface	launchDiffExprLoader
View and plot results via a visual interface	launchDrugSetEnrichmentAnalyser
View metadata via a visual interface	launchMetadataViewer
View and plot results via a visual interface	launchResultPlotter
List available gene expression and drug sensitivity correlation matrices	listExpressionDrugSensitivityAssociation
Load CMap data	loadCMapData
Load matrix of CMap perturbation's differential expression z-scores (optional)	loadCMapZscores
Load table with drug descriptors	loadDrugDescriptors
Load ENCODE samples	loadENCODEsamples
Load gene expression and drug sensitivity correlation matrix	loadExpressionDrugSensitivityAssociation
Parse CMap identifier	parseCMapID
Perform differential gene expression based on ENCODE data	performDifferentialExpression
Operations on a 'perturbationChanges' object	dim.perturbationChanges dimnames.perturbationChanges plot.perturbationChanges [.perturbationChanges
Plot data comparison	plot.referenceComparison
Plot drug set enrichment	plotDrugSetEnrichment
Plot similar perturbations against predicted targeting drugs	plotTargetingDrugsVSsimilarPerturbations
Predict targeting drugs	predictTargetingDrugs
Prepare CMap perturbation data	prepareCMapPerturbations
Prepare drug sets from a table with compound descriptors	prepareDrugSets
Load ENCODE gene expression data	prepareENCODEgeneExpression
Print a 'similarPerturbations' object	print.similarPerturbations
Rank differential expression profile against CMap perturbations by similarity	compareAgainstCMap rankSimilarPerturbations