Package: knowYourCG 1.3.15

Goldberg David

knowYourCG: Functional analysis of DNA methylome datasets

KnowYourCG (KYCG) is a supervised learning framework designed for the functional analysis of DNA methylation data. Unlike existing tools that focus on genes or genomic intervals, KnowYourCG directly targets CpG dinucleotides, featuring automated supervised screenings of diverse biological and technical influences, including sequence motifs, transcription factor binding, histone modifications, replication timing, cell-type-specific methylation, and trait-epigenome associations. KnowYourCG addresses the challenges of data sparsity in various methylation datasets, including low-pass Nanopore sequencing, single-cell DNA methylomes, 5-hydroxymethylation profiles, spatial DNA methylation maps, and array-based datasets for epigenome-wide association studies and epigenetic clocks.

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

knowYourCG_1.3.15.tar.gz
knowYourCG_1.3.15.zip(r-4.5)knowYourCG_1.3.15.zip(r-4.4)
knowYourCG_1.3.15.tgz(r-4.4-x86_64)knowYourCG_1.3.15.tgz(r-4.4-arm64)
knowYourCG_1.3.15.tar.gz(r-4.5-noble)knowYourCG_1.3.15.tar.gz(r-4.4-noble)
knowYourCG_1.3.8.tgz(r-4.4-emscripten)
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

Uses libs:
  • zlib– Compression library

On BioConductor:knowYourCG-1.3.13(bioc 3.21)knowYourCG-1.2.5(bioc 3.20)

epigeneticsdnamethylationsequencingsinglecellspatialmethylationarrayzlib

6.21 score 2 stars 4 scripts 107 downloads 22 exports 88 dependencies

Last updated 17 days agofrom:48d831c362. Checks:1 OK, 5 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 05 2025
R-4.5-win-x86_64ERRORJan 05 2025
R-4.5-linux-x86_64ERRORJan 05 2025
R-4.4-win-x86_64ERRORJan 05 2025
R-4.4-mac-x86_64ERRORJan 05 2025
R-4.4-mac-aarch64ERRORJan 05 2025

Exports:aggregateTestEnrichmentsannoProbesbuildGeneDBsdbStatsgetDBsKYCG_plotBarKYCG_plotDotKYCG_plotEnrichAllKYCG_plotLollipopKYCG_plotManhattanKYCG_plotMetaKYCG_plotMetaEnrichmentKYCG_plotPointRangeKYCG_plotSetEnrichmentKYCG_plotVolcanoKYCG_plotWaterfalllistDBGroupstestEnrichmenttestEnrichment2testEnrichmentSEAtestGOtestProbeProximity

Dependencies:AnnotationDbiAnnotationHubaskpassBiobaseBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicliprcolorspacecpp11crayoncurlDBIdbplyrdplyrExperimentHubfansifarverfastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegtablehmshttrIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppreadrreshape2rlangRSQLiteS4VectorsscalessesameDatastringistringrsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwheatmapwithrXVectoryaml

Functional Analysis of DNAm Sequencing Data

Rendered fromSequencing.Rmdusingknitr::rmarkdownon Jan 05 2025.

Last update: 2024-12-30
Started: 2024-12-20

Functional Analysis of DNAm Array Data

Rendered fromArray.Rmdusingknitr::rmarkdownon Jan 05 2025.

Last update: 2024-12-25
Started: 2024-12-20

Continuous Data Analysis

Rendered fromContinuous.Rmdusingknitr::rmarkdownon Jan 05 2025.

Last update: 2024-12-30
Started: 2024-12-20

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 query in knowledgebase setstestEnrichment
Test enrichment from YAME-compressed CG setstestEnrichment2
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