Package: knowYourCG 1.3.0

Goldberg David

knowYourCG: Functional analysis of DNA methylome datasets

knowYourCG automates the functional analysis of DNA methylation data. The package tests the enrichment of discrete CpG probes across thousands of curated biological and technical features. GSEA-like analysis can be performed on continuous methylation data query sets. knowYourCG can also take beta matrices as input to perform feature aggregation over the curated database sets.

Authors:Zhou Wanding [aut], Goldberg David [aut, cre], Fu Hongxiang [ctb], Moyer Ethan [ctb]

knowYourCG_1.3.0.tar.gz
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knowYourCG_1.3.0.tgz(r-4.4-any)knowYourCG_1.1.0.tgz(r-4.3-any)
knowYourCG_1.3.0.tar.gz(r-4.5-noble)knowYourCG_1.3.0.tar.gz(r-4.4-noble)
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knowYourCG.pdf |knowYourCG.html✨
knowYourCG/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/zhou-lab/knowyourcg/issues

On BioConductor:knowYourCG-1.3.0(bioc 3.21)knowYourCG-1.2.0(bioc 3.20)

epigeneticsdnamethylationmethylationarray

5.32 score 1 stars 2 scripts 170 downloads 10 exports 72 dependencies

Last updated 22 days agofrom:1aa1f93b14. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winERROROct 31 2024
R-4.5-linuxERROROct 31 2024
R-4.4-winERROROct 31 2024
R-4.4-macERROROct 31 2024
R-4.3-winERRORSep 28 2024
R-4.3-macERRORSep 28 2024

Exports:aggregateTestEnrichmentsannoProbesbuildGeneDBsdbStatsgetDBslistDBGroupstestEnrichmenttestEnrichmentSEAtestGOtestProbeProximity

Dependencies:AnnotationDbiAnnotationHubaskpassBiobaseBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicliprcpp11crayoncurlDBIdbplyrdplyrExperimentHubfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehmshttrIRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6rappdirsRcppreadrreshape2rlangRSQLiteS4VectorssesameDatastringistringrsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXVectoryamlzlibbioc

knowYourCG

Rendered fromKYCG.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-03-27
Started: 2023-08-17

Readme and manuals

Help Manual

Help pageTopics
Aggregate test enrichment resultsaggregateTestEnrichments
Annotate Probe IDs using KYCG databasesannoProbes
build gene-probe association databasebuildGeneDBs
dbStats aggregates methylation of a given betas matrix over specified database set featuresdbStats
Get databases by full or partial names of the database group(s)getDBs
Bar plot to show most enriched CG groups from testEnrichmentKYCG_plotBar
Dot plot to show most enriched CG groups from testEnrichmentKYCG_plotDot
plot enrichment test resultKYCG_plotEnrichAll
creates a lollipop plot of log(estimate) given data with fields estimate.KYCG_plotLollipop
KYCG_plotManhattan makes a manhattan plot to summarize EWAS resultsKYCG_plotManhattan
Plot meta gene or other meta genomic featuresKYCG_plotMeta
Plot meta gene or other meta genomic featuresKYCG_plotMetaEnrichment
Plot point range for a list of enrichment testing results against the same set of databasesKYCG_plotPointRange
Plot Set EnrichmentKYCG_plotSetEnrichment
creates a volcano plot of -log2(p.value) and log(estimate) given data with fields estimate and p.value.KYCG_plotVolcano
create a waterfall plot of log(estimate) given test enrichmentKYCG_plotWaterfall
List database group nameslistDBGroups
testEnrichment tests for the enrichment of a set of probes (query set) in a number of features (database sets).testEnrichment
testEnrichmentFisher uses Fisher's exact test to estimate the association between two categorical variables.testEnrichmentFisher
uses the GSEA-like test to estimate the association of a categorical variable against a continuous variable.testEnrichmentSEA
testEnrichmentSpearman uses the Spearman statistical test to estimate the association between two continuous variables.testEnrichmentSpearman
tests Gene Ontology of genes overlapping CpG querytestGO
testProbeProximity tests if a query set of probes share closer genomic proximity than if randomly distributedtestProbeProximity