Package: signifinder 1.15.0

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 coming from public literature, based on gene expression values, and return single-sample (-cell/-spot) scores. Currently, signifinder collects more than 70 distinct signatures, relating to multiple tumors and multiple cancer processes.

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

signifinder_1.15.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
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-1.15.0(bioc 3.24)signifinder-1.13.0(bioc 3.23)

geneexpression genetarget immunooncology biomedicalinformatics rnaseq microarray reportwriting visualization singlecell spatial genesignaling

4.88 score 9 stars 21 scripts 339 downloads 58 exports 246 dependencies

Last updated from:12aa3a5d74. Checks:1 NOTE, 8 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	376
linux-devel-x86_64	ERROR	984
source / vignettes	ERROR	522
linux-release-x86_64	ERROR	1010
macos-release-arm64	ERROR	682
macos-oldrel-arm64	ERROR	868
windows-devel	ERROR	1090
windows-release	ERROR	779
windows-oldrel	ERROR	964
wasm-release	OK	371

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 BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocParallel BiocSingular biomaRt Biostrings bit bit64 bitops blob boot bootstrap broom cachem car carData cigarillo circlize class cli clipr clue cluster codetools colorspace commonmark ComplexHeatmap consensusOV corrplot cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats Deriv DGEobj DGEobj.utils diagram digest dir.expiry doBy doParallel dplyr e1071 ensembldb exactRankTests farver fastmap filelock foreach forecast formatR Formula fracdiff futile.logger futile.options future future.apply gdata genefu generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggplot2 ggpubr ggrepel ggridges ggsci ggsignif ggtext GlobalOptions globals glue graph gridExtra gridtext GSEABase GSVA gtable gtools h5mread HDF5Array hms httr httr2 iC10 iC10TrainingData impute ipred IRanges irlba isoband iterators jpeg jsonlite KEGGREST KernSmooth labeling lambda.r lattice lava lazyeval lifecycle limma listenv litedown lme4 lmtest lubridate magick magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats maxstat mclust memoise memuse mgcv microbenchmark mime minqa modelr mvtnorm nlme nloptr nnet numDeriv openair openssl org.Hs.eg.db pamr parallelly patchwork pbkrtest pillar pkgconfig png polynom prettyunits prodlim progress progressr ProtGenerics proxy purrr quantreg R6 randomForest rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack readr reformulas restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmeta rpart Rsamtools RSQLite rstatix rsvd rtracklayer S4Arrays S4Vectors S7 ScaledMatrix scales Seqinfo shape SingleCellExperiment snow SparseArray SparseM sparseMatrixStats SpatialExperiment SQUAREM statmod stringi stringr SummarizedExperiment SuppDists survcomp survival survivalROC survminer sys tibble tidyr tidyselect timechange timeDate TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene tzdb UCSC.utils urca utf8 vctrs viridis viridisLite vroom withr xfun XML xml2 xtable XVector yaml zoo

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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

Package: signifinder 1.15.0

signifinder: Collection and implementation of public transcriptional cancer signatures

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