Package: signifinder 1.9.1

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-1.9.0(bioc 3.21)signifinder-1.7.0(bioc 3.20)

geneexpression genetarget immunooncology biomedicalinformatics rnaseq microarray reportwriting visualization singlecell spatial genesignaling

6.27 score 7 stars 16 scripts 126 downloads 54 exports 267 dependencies

Last updated 4 days agofrom:fdd97a7d33. Checks:OK: 1 ERROR: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 18 2024
R-4.5-win	ERROR	Dec 18 2024
R-4.5-linux	ERROR	Dec 18 2024
R-4.4-win	ERROR	Dec 18 2024
R-4.4-mac	ERROR	Dec 18 2024
R-4.3-win	ERROR	Dec 18 2024
R-4.3-mac	ERROR	Dec 18 2024

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

Dependencies:abind AIMS amap annotate AnnotationDbi AnnotationFilter askpass assertthat assorthead babelgene backports base64enc beachmat BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel BiocSet BiocSingular biomaRt Biostrings bit bit64 bitops blob boot bootstrap broom bslib cachem car carData checkmate circlize class cli clipr clue cluster codetools colorspace commonmark ComplexHeatmap consensusOV corrplot cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir Deriv DGEobj DGEobj.utils diagram digest doBy doParallel dplyr e1071 edgeR ensembldb evaluate exactRankTests fansi farver fastmap filelock fontawesome foreach formatR Formula fs 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 htmltools htmlwidgets httr httr2 iC10 iC10TrainingData impute interp ipred IRanges irlba isoband iterators jpeg jquerylib jsonlite KEGGREST KernSmooth km.ci KMsurv knitr labeling lambda.r later lattice latticeExtra lava lazyeval lifecycle limma listenv lme4 locfit 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 ontologyIndex openair openssl org.Hs.eg.db pamr parallelly patchwork pbkrtest pillar pkgconfig plogr plotly plyr png polynom prettyunits prodlim progress progressr promises ProtGenerics proxy purrr quantreg R6 randomForest rappdirs RColorBrewer Rcpp RcppEigen RCurl readr restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rmeta rpart Rsamtools RSQLite rstatix rsvd rtracklayer S4Arrays S4Vectors sass ScaledMatrix scales shape SingleCellExperiment snow sparrow SparseArray SparseM sparseMatrixStats SpatialExperiment SQUAREM statmod stringi stringr SummarizedExperiment SuppDists survcomp survival survivalROC survminer survMisc sys tibble tidyr tidyselect timechange tinytex 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 zlibbioc zoo

signifinder vignette

Stefania Pirrotta, Enrica Calura

Rendered fromsignifinder.Rmdusingknitr::rmarkdownon Dec 18 2024.

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
Breast Cancer Cellular States Signature	breastStateSign
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
Glioblastoma Cellular States Signature	glioCellStateSign
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
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
Metastatic Melanoma Cellular States Signature	melStateSign
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
passON Signature	PassONSign
Pyroptosis Signature	pyroptosisSign
Ridgeline Plot	ridgelineSignPlot
CD49fHi Basal Stem Cell Signature	stemCellCD49fSign
Survival Plot	survivalSignPlot
Pan-Fibroblast TGFB Response Signature	TGFBSign
TinflamSign Signature	TinflamSign
Tertiary Lymphoid Structures (TLS) Signature	TLSSign
VEGF Signature	VEGFSign