Package: signifinder 1.9.3

Stefania Pirrotta

signifinder: Collection and implementation of public transcriptional cancer signatures

signifinder is an R package for computing and exploring a compendium of tumor signatures. It allows to compute a variety of signatures, based on gene expression values, and return single-sample scores. Currently, signifinder contains more than 60 distinct signatures collected from the literature, relating to multiple tumors and multiple cancer processes.

Authors:Stefania Pirrotta [cre, aut], Enrica Calura [aut]

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

# Install 'signifinder' in R:

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

Bug tracker:https://github.com/caluralab/signifinder/issues

Datasets:

ovse - Example expression data.

On BioConductor:signifinder-1.9.3(bioc 3.21)signifinder-1.7.0(bioc 3.20)

geneexpression genetarget immunooncology biomedicalinformatics rnaseq microarray reportwriting visualization singlecell spatial genesignaling

6.44 score 7 stars 15 scripts 126 downloads 58 exports 247 dependencies

Last updated 9 days agofrom:c426fddb2d. Checks:1 OK, 6 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 16 2025
R-4.5-win	NOTE	Jan 16 2025
R-4.5-linux	NOTE	Jan 16 2025
R-4.4-win	NOTE	Jan 16 2025
R-4.4-mac	NOTE	Jan 16 2025
R-4.3-win	NOTE	Jan 16 2025
R-4.3-mac	NOTE	Jan 16 2025

Exports:ADOSign APMSign ASCSign autophagySign availableSignatures CD39CD8TcellSign cellCycleSign chemokineSign CINSign CISSign CombinedSign consensusOVSign correlationSignPlot COXISSign DNArepSign ECMSign EMTSign evaluationSignPlot expandedImmuneSign ferroptosisSign geneHeatmapSignPlot getSignGenes glycolysisSign heatmapSignPlot HRDSSign hypoxiaSign ICBResponseSign IFNSign immuneCytSign immunoScoreSign interferonSign IPRESSign IPSOVSign IPSSign IRGSign ISCSign lipidMetabolismSign LRRC15CAFSign matrisomeSign metalSign MITFlowPTENnegSign mitoticIndexSign MPSSign multipleSign oneSignPlot oxphosSign PassONSign pyroptosisSign ridgelineSignPlot SCSubtypeSign stateSign stemCellCD49fSign stressSign survivalSignPlot TGFBSign TinflamSign TLSSign VEGFSign

Dependencies:abind AIMS amap annotate AnnotationDbi AnnotationFilter askpass assertthat assorthead backports beachmat BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel BiocSingular biomaRt Biostrings bit bit64 bitops blob boot bootstrap broom cachem car carData circlize class cli clipr clue cluster codetools colorspace commonmark ComplexHeatmap consensusOV corrplot cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir Deriv DGEobj DGEobj.utils diagram digest doBy doParallel dplyr e1071 ensembldb evaluate exactRankTests fansi farver fastmap filelock foreach formatR Formula futile.logger futile.options future future.apply gdata genefu generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggplot2 ggpubr ggrepel ggridges ggsci ggsignif ggtext GlobalOptions globals glue graph gridExtra gridtext GSEABase GSVA gtable gtools HDF5Array hexbin highr hms httr httr2 iC10 iC10TrainingData impute interp ipred IRanges irlba isoband iterators jpeg jsonlite KEGGREST KernSmooth km.ci KMsurv knitr labeling lambda.r lattice latticeExtra lava lazyeval lifecycle limma listenv lme4 lubridate magick magrittr mapproj maps markdown MASS Matrix MatrixGenerics MatrixModels matrixStats maxstat mclust memoise mgcv microbenchmark mime minqa modelr munsell mvtnorm nlme nloptr nnet numDeriv openair openssl org.Hs.eg.db pamr parallelly patchwork pbkrtest pillar pkgconfig plogr png polynom prettyunits prodlim progress progressr ProtGenerics proxy purrr quantreg R6 randomForest rappdirs rbibutils RColorBrewer Rcpp RcppEigen RCurl Rdpack readr reformulas restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmeta rpart Rsamtools RSQLite rstatix rsvd rtracklayer S4Arrays S4Vectors ScaledMatrix scales shape SingleCellExperiment snow SparseArray SparseM sparseMatrixStats SpatialExperiment SQUAREM statmod stringi stringr SummarizedExperiment SuppDists survcomp survival survivalROC survminer survMisc sys tibble tidyr tidyselect timechange TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene tzdb UCSC.utils utf8 vctrs viridis viridisLite vroom withr xfun XML xml2 xtable XVector yaml zoo

signifinder vignette

Stefania Pirrotta, Enrica Calura

Rendered fromsignifinder.Rmdusingknitr::rmarkdownon Jan 16 2025.

Last update: 2024-04-19
Started: 2022-06-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Adenosine Signaling Signature	ADOSign
Antigen Processing Machinery Signature	APMSign
Adult Stem Cell Signature	ASCSign
Autophagy Signature	autophagySign
Show Available Signatures	availableSignatures
CD39+ CD8+ T cells Signature	CD39CD8TcellSign
Cell-cycle Signature classifier	cellCycleSign
Chemokine Signature	chemokineSign
Chromosomal instability Signature	CINSign
CIS (carcinoma-in situ) Signature	CISSign
EMT-Inflammation Combined Signature	CombinedSign
ConsensusOV Signature	consensusOVSign
Correlation Plot	correlationSignPlot
COX-2-associated Inflammatory Signature	COXISSign
DNA Repair Signature	DNArepSign
Extracellular Matrix Signature	ECMSign
Epithelial-Mesenchymal Transition Signature	EMTSign
Evaluation Plot	evaluationSignPlot
ExpandedImmune Signature	expandedImmuneSign
Ferroptosis Signature	ferroptosisSign
Genes' Signatures' Heatmap	geneHeatmapSignPlot
Get Signature Gene List	getSignGenes
Glycolysis Signature	glycolysisSign
Global Heatmap of Signatures' scores.	heatmapSignPlot
Homologous Recombination Deficiency Signature	HRDSSign
Hypoxia Signature	hypoxiaSign
ICB Response Signature	ICBResponseSign
IFN-gamma Signature	IFNSign
Immune Cytolytic Activity Signature	immuneCytSign
Immunogenic Signature	immunoScoreSign
Interferon Signature	interferonSign
IPRES Signature	IPRESSign
IPSOV Signature	IPSOVSign
ImmunoPhenoScore Signature	IPSSign
Immune-Related Genes Signature	IRGSign
Adult Intestinal Stem Cell Signature	ISCSign
Lipid Metabolism Signature	lipidMetabolismSign
LRRC15 CAF Signature	LRRC15CAFSign
Core Matrisome Gene signature	matrisomeSign
Metal Response Signature	metalSign
MITFlow/PTENneg Signature	MITFlowPTENnegSign
Mitotic Index	mitoticIndexSign
Melanocytic Plasticity Signature	MPSSign
Multiple Signatures Computation	multipleSign
Scatterplot for a single signature	oneSignPlot
Example expression data.	ovse
Oxidative Phosphorylation Signature	oxphosSign
passON Signature	PassONSign
Pyroptosis Signature	pyroptosisSign
Ridgeline Plot	ridgelineSignPlot
Breast Cancer Subtypes Signature	SCSubtypeSign
Cellular States Signature	stateSign
CD49fHi Basal Stem Cell Signature	stemCellCD49fSign
Stress Response Signature	stressSign
Survival Plot	survivalSignPlot
Pan-Fibroblast TGFB Response Signature	TGFBSign
TinflamSign Signature	TinflamSign
Tertiary Lymphoid Structures (TLS) Signature	TLSSign
VEGF Signature	VEGFSign