Package: HiBED 1.11.0

Ze Zhang

HiBED: HiBED

Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation. The HiBED deconvolution estimates proportions up to 7 cell types (GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells) in bulk brain tissues.

Authors:Ze Zhang [cre, aut], Lucas A. Salas [aut]

HiBED_1.11.0.tar.gz
HiBED_1.11.0.tar.gz(r-4.7-any)HiBED_1.11.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HiBED/json (API)

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

Bug tracker:https://github.com/salaslab/hibed/issues

Datasets:
  • HiBED_Libraries - HiBED library CpGs matrix stored in SummarizedExperiment for brain tissue DNA methylation deconvolution

On BioConductor:HiBED-1.11.0(data/experiment 3.24)HiBED-1.10.0(data/experiment 3.23)

experimentdatahomo_sapiens_datatissuemicroarraydatagenomemethylationarraydatapackagetypedatadatapkg

3.30 score 2 stars 5 scripts 1 exports 144 dependencies

Last updated from:65a76d752b. Checks:1 NOTE, 2 WARNING, 1 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE201
linux-develWARNING1468
source / vignettesERROR338
linux-releaseWARNING584

Exports:HiBED_deconvolution

Dependencies:abindannotateAnnotationDbiAnnotationHubaskpassbase64beanplotBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobbumphuntercachemcigarilloclicliprcodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdir.expirydoRNGdplyrExperimentHubfastmapfilelockFlowSorted.Blood.EPICFlowSorted.DLPFC.450kforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryglueh5mreadHDF5Arrayhmshttrhttr2illuminaioIRangesiteratorsjsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimeminfimulttestnlmenor1mixopensslpillarpkgconfigplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshaperestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsscrimeselectrSeqinfosiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbutf8vctrsvroomwithrXMLxml2xtableXVectoryaml