Package: TBSignatureProfiler 1.25.0

Kiloni Quiles

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

TBSignatureProfiler_1.25.0.tar.gz
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TBSignatureProfiler_1.25.0.tgz(r-4.6-any)TBSignatureProfiler_1.25.0.tgz(r-4.5-any)
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TBSignatureProfiler_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
TBSignatureProfiler/json (API)

# Install 'TBSignatureProfiler' in R:

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

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

Pkgdown/docs site:https://wejlab.github.io

Datasets:

common_sigAnnotData - Annotation information for published TB signatures.
COVIDsignatures - A list of published/pre-print COVID-19 signatures.
OriginalTrainingData - Discovery datasets for corresponding gene signatures.
sigAnnotData - Annotation information for published TB 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.

On BioConductor:TBSignatureProfiler-1.25.0(bioc 3.24)TBSignatureProfiler-1.24.0(bioc 3.23)

geneexpression differentialexpression bioconductor-package biomarkers gene-signatures tuberculosis

7.49 score 13 stars 53 scripts 2 mentions 17 exports 173 dependencies

Last updated from:3f57ba4f0c. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	208
linux-devel-x86_64	OK	352
source / vignettes	OK	280
linux-release-x86_64	OK	352
macos-release-arm64	OK	140
macos-oldrel-arm64	OK	162
windows-devel	OK	202
windows-release	OK	203
windows-oldrel	OK	213
wasm-release	OK	239

Exports:bootstrapAUC compareAlgs compareBoxplots deseq2_norm_rle distinctColors evaluateOriginalModel mkAssay plotQuantitative runTBsigProfiler signatureBoxplot signatureGeneHeatmap signatureHeatmap SignatureQuantitative signatureROCplot signatureROCplot_CI tableAUC TBSPapp

Dependencies:abind annotate AnnotationDbi askpass ASSIGN assorthead base64enc beachmat BH Biobase BiocFileCache BiocGenerics biocmake BiocParallel BiocSingular Biostrings bit bit64 bitops blob bslib cachem caTools circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats DESeq2 digest dir.expiry doParallel dplyr DT edgeR evaluate expm farver fastmap filelock fontawesome foreach formatR fs futile.logger futile.options gdata genefilter generics GenomicRanges GetoptLong ggplot2 ggrepel glmnet GlobalOptions glue gplots graph GSEABase GSVA gtable gtools h5mread HDF5Array HGNChelper highr htmltools htmlwidgets httr httr2 IRanges irlba isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit magick magrittr Matrix MatrixGenerics matrixStats memoise memuse mgcv mime msm mvtnorm nlme openssl otel pillar pkgconfig plotly plyr png pROC promises purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reshape reshape2 rhdf5 rhdf5filters Rhdf5lib rjson Rlab rlang rmarkdown ROCit RSQLite rsvd S4Arrays S4Vectors S7 sass ScaledMatrix scales Seqinfo shape SingleCellExperiment singscore snow SparseArray sparseMatrixStats SpatialExperiment splitstackshape statmod stringi stringr SummarizedExperiment survival sva sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun XML xtable XVector yaml

Introduction to the TBSignatureProfiler

Rendered fromtbspVignetteT.Rmdusingknitr::rmarkdown

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

Help page	Topics
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

Package: TBSignatureProfiler 1.25.0

TBSignatureProfiler: Profile RNA-Seq Data Using TB Pathway Signatures

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