Package: TBSignatureProfiler 1.19.0

Aubrey R. Odom

TBSignatureProfiler: Profile RNA-Seq Data Using TB Pathway Signatures

Gene signatures of TB progression, TB disease, and other TB disease states have been validated and published previously. This package aggregates known signatures and provides computational tools to enlist their usage on other datasets. The TBSignatureProfiler makes it easy to profile RNA-Seq data using these signatures and includes common signature profiling tools including ASSIGN, GSVA, and ssGSEA. Original models for some gene signatures are also available. A shiny app provides some functionality alongside for detailed command line accessibility.

Authors:Aubrey R. Odom [aut, cre, dtm], David Jenkins [aut, org], Xutao Wang [aut], Yue Zhao [ctb], Christian Love [ctb], W. Evan Johnson [aut]

TBSignatureProfiler_1.19.0.tar.gz
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TBSignatureProfiler.pdf |TBSignatureProfiler.html✨
TBSignatureProfiler/json (API)

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

Peer review:

Bug tracker:https://github.com/wejlab/tbsignatureprofiler/issues

Pkgdown:https://wejlab.github.io

Datasets:
  • COVIDsignatures - A list of published/pre-print COVID-19 signatures.
  • OriginalTrainingData - Discovery datasets for corresponding gene signatures.
  • TB_hiv - An example TB dataset with TB/HIV data.
  • TB_indian - An example TB dataset with Indian population data.
  • TBcommon - A list of published TB signatures, using author-given names.
  • TBsignatures - A list of published TB signatures.
  • TBsignaturesSplit - Up/Down-regulated genes information for selected TB signatures.
  • common_sigAnnotData - Annotation information for published TB signatures.
  • sigAnnotData - Annotation information for published TB signatures.

On BioConductor:TBSignatureProfiler-1.19.0(bioc 3.21)TBSignatureProfiler-1.17.1(bioc 3.20)

geneexpressiondifferentialexpressionbioconductor-packagebiomarkersgene-signaturestuberculosis

7.28 score 12 stars 20 scripts 178 downloads 2 mentions 17 exports 174 dependencies

Last updated 2 days agofrom:d7f3c8a7bb. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winOKDec 19 2024
R-4.5-linuxOKDec 19 2024
R-4.4-winOKDec 19 2024
R-4.4-macOKDec 19 2024
R-4.3-winOKOct 06 2024
R-4.3-macOKOct 06 2024

Exports:bootstrapAUCcompareAlgscompareBoxplotsdeseq2_norm_rledistinctColorsevaluateOriginalModelmkAssayplotQuantitativerunTBsigProfilersignatureBoxplotsignatureGeneHeatmapsignatureHeatmapSignatureQuantitativesignatureROCplotsignatureROCplot_CItableAUCTBSPapp

Dependencies:abindannotateAnnotationDbiaskpassASSIGNassortheadbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiocSingularBiostringsbitbit64bitopsblobbslibcachemcaToolscirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsDESeq2digestdoParalleldplyrDTedgeRevaluateexpmfansifarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgdatagenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2ggrepelglmnetGlobalOptionsgluegplotsgraphGSEABaseGSVAgtablegtoolsHDF5ArrayHGNChelperhighrhtmltoolshtmlwidgetshttpuvhttrIRangesirlbaisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemsmmunsellmvtnormnlmeopensslpillarpkgconfigplogrplotlyplyrpngpROCpromisespurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreshapereshape2rhdf5rhdf5filtersRhdf5librjsonRlabrlangrmarkdownROCitRSQLitersvdS4ArraysS4VectorssassScaledMatrixscalesshapeSingleCellExperimentsingscoresnowSparseArraysparseMatrixStatsSpatialExperimentsplitstackshapestatmodstringistringrSummarizedExperimentsurvivalsvasystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxtableXVectoryamlzlibbioc

Introduction to the TBSignatureProfiler

Aubrey Odom, W. Evan Johnson

Rendered fromtbspVignetteT.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2024-12-18
Started: 2024-12-18

Readme and manuals

Help Manual

Help pageTopics
TB gene signatures that do not require retraining..OriginalModel_NoRetraining
TB gene signatures that require retraining..OriginalModel_Retraining
Introduce a new signature into the TBSignatureProfiler.addTBsignature
Bootstrap on Leave-one-out CV with Logistic Regression.Bootstrap_LOOCV_LR_AUC
Bootstrap the AUC and conduct T-Tests for a collection of signatures.bootstrapAUC
Annotation information for published TB signatures.common_sigAnnotData
Compare scoring algorithms on a single signature via heatmap or boxplot.compareAlgs
Create a comparison plot of boxplots for bootstrapped AUC values.compareBoxplots
A list of published/pre-print COVID-19 signatures.COVIDsignatures
Train original model for gene signatures Leong_24, Leong_RISK_29, Zhao_NANO_6 using lasso logistic regression.cv_glmnet_OriginalModel
Normalize gene expression count data.deseq2_norm_rle
Generate a distinct palette for coloring different clusters.distinctColors
A function that implements the original methods for multiple TB signatures.evaluateOriginalModel
Train original model for gene signatures Berry_393 and Berry_OD_86.knn_OriginalModel
Train original model for gene signatures Jacobsen_3 and Sambarey_HIV_10.lda_OriginalModel
Perform Leave-one-out CV with Logistic Regression.LOOAUC_simple_multiple_noplot_one_df
Add SummarizedExperiment assays to the data structure.mkAssay
Obtain training data, testing data, and train signature's original model.ObtainSampleScore_OriginalModel
Discovery datasets for corresponding gene signatures.OriginalTrainingData
Create a boxplot using logistic regression and bootstrap LOOCV to evaluate signatures.plotQuantitative
Train original model for gene signatures Maertzdorf_4, Maertzdorf_15, Verhagen_10, and LauxdaCosta_OD_3.randomForest_OriginalModel
A function for reference batch correction and imputation.ref_combat_impute
Run TB gene signature profiling.runTBsigProfiler
Annotation information for published TB signatures.sigAnnotData
Plot a boxplot of signature genes.signatureBoxplot
Plot a heatmap of a single signature score with individual gene expression levels.signatureGeneHeatmap
Plot a heatmap of signature scores.signatureHeatmap
Use logistic regression and bootstrap LOOCV to evaluate signatures.SignatureQuantitative
Create an array of ROC plots to compare signatures.signatureROCplot
Create an array of ROC plots with confidence interval bands to compare signatures.signatureROCplot_CI
Filter gene expression value matrix based on certain gene sets.subsetGeneSet
Train original model gene signature Suliman_RISK_4.SulimanOriginalModel
Train original model for gene signatures Bloom_OD_144 and Zak_RISK_16.svm_OriginalModel
Create a table of results for t-tests and bootstrapped AUCs for multiple scored signatures.tableAUC
An example TB dataset with TB/HIV data.TB_hiv
An example TB dataset with Indian population data.TB_indian
A list of published TB signatures, using author-given names.TBcommon
A list of published TB signatures.TBsignatures
Up/Down-regulated genes information for selected TB signatures.TBsignaturesSplit
Run the TBSignatureProfiler Shiny application.TBSPapp