Package: recountmethylation 1.17.0
Sean K Maden
recountmethylation: Access and analyze public DNA methylation array data compilations
Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina's Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info.
Authors:
recountmethylation_1.17.0.tar.gz
recountmethylation_1.17.0.zip(r-4.5)recountmethylation_1.17.0.zip(r-4.4)recountmethylation_1.17.0.zip(r-4.3)
recountmethylation_1.17.0.tgz(r-4.4-any)recountmethylation_1.17.0.tgz(r-4.3-any)
recountmethylation_1.17.0.tar.gz(r-4.5-noble)recountmethylation_1.17.0.tar.gz(r-4.4-noble)
recountmethylation_1.17.0.tgz(r-4.4-emscripten)recountmethylation_1.17.0.tgz(r-4.3-emscripten)
recountmethylation.pdf |recountmethylation.html✨
recountmethylation/json (API)
NEWS
| # Install 'recountmethylation' in R: |
| install.packages('recountmethylation', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/metamaden/recountmethylation/issues
On BioConductor:recountmethylation-1.17.0(bioc 3.21)recountmethylation-1.16.0(bioc 3.20)
dnamethylationepigeneticsmicroarraymethylationarrayexperimenthub
Last updated 2 months agofrom:873438ed36. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | NOTE | Nov 30 2024 |
| R-4.5-linux | NOTE | Nov 30 2024 |
| R-4.4-win | NOTE | Nov 30 2024 |
| R-4.4-mac | NOTE | Nov 30 2024 |
| R-4.3-win | NOTE | Nov 30 2024 |
| R-4.3-mac | NOTE | Nov 30 2024 |
Exports:bactrlbathreshdata_mdpostgds_idat2rggds_idatqueryget_crossreactive_cpgsget_qcsignalget_rmdlget_servermatrixgetdb_h5_rggetdb_h5_testgetdb_h5se_gmgetdb_h5se_grgetdb_h5se_rggetdb_h5se_testgetrghreadmatchds_1to2rgseservermatrixsmfilt
Dependencies:abindannotateAnnotationDbiaskpassbase64basiliskbasilisk.utilsbeanplotBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemclicliprcodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdir.expirydoRNGdplyrfansifastmapfilelockforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryglueHDF5Arrayherehmshttrhttr2illuminaioIRangesiteratorsjsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimeminfimulttestnlmenor1mixopensslpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppTOMLRCurlreadrrentrezreshaperestfulrreticulaterhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsrprojrootRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsscrimeselectrsiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXMLxml2xtableXVectoryamlzlibbioc
Data Analyses
Rendered fromrecountmethylation_data_analyses.Rmdusingknitr::rmarkdownon Nov 30 2024.Last update: 2023-03-27
Started: 2020-07-13
Determine population ancestry from DNAm arrays
Rendered fromrecountmethylation_glint.Rmdusingknitr::rmarkdownon Nov 30 2024.Last update: 2022-03-04
Started: 2022-03-04
Nearest neighbors analysis for DNAm arrays
Rendered fromrecountmethylation_search_index.Rmdusingknitr::rmarkdownon Nov 30 2024.Last update: 2023-03-27
Started: 2022-02-28
Power analysis for DNAm arrays
Rendered fromrecountmethylation_pwrewas.Rmdusingknitr::rmarkdownon Nov 30 2024.Last update: 2022-03-04
Started: 2022-02-28
Practical uses for provided CpG probe annotations
Rendered fromcpg_probe_annotations.Rmdusingknitr::rmarkdownon Nov 30 2024.Last update: 2024-02-01
Started: 2023-03-27
recountmethylation User's Guide
Rendered fromrecountmethylation_users_guide.Rmdusingknitr::rmarkdownon Nov 30 2024.Last update: 2023-03-26
Started: 2020-07-13
Working with DNAm data types
Rendered fromexporting_saving_data.Rmdusingknitr::rmarkdownon Nov 30 2024.Last update: 2023-03-27
Started: 2023-03-27
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ba.background | ba.background ba.biotinstaining.grn ba.biotinstaining.red ba.bisulfiteconv1.grn ba.bisulfiteconv1.red ba.bisulfiteconv2 ba.extension.grn ba.extension.red ba.hybridization.hi.vs.med ba.hybridization.med.vs.low ba.nonpolymorphic.grn ba.nonpolymorphic.red ba.restoration ba.specificity1.grn ba.specificity1.red ba.specificity2 ba.targetremoval1 ba.targetremoval2 |
| bactrl | bactrl |
| Get BeadArray control outcomes from a matrix of metric signals | bathresh |
| Retrieve all available sample metadata from an HDF5 database. | data_mdpost |
| Get IDATs as an RGChannelSet from GEO/GDS | gds_idat2rg |
| Query and download IDATs from GEO Data Sets | gds_idatquery |
| get_crossreactive_cpgs | get_crossreactive_cpgs |
| get_fh | get_fh |
| get_qcsignal | get_qcsignal |
| Get DNAm assay data. | get_rmdl |
| get_servermatrix | get_servermatrix |
| Access database files. | getdb getdb_h5se_gm getdb_h5se_gr getdb_h5se_rg getdb_h5se_test getdb_h5_rg getdb_h5_test |
| Query and store data from h5 file signal tables | getrg |
| Query and store an HDF5 dataset on row and column indices. | hread |
| make_si | make_si |
| Match two datasets on rows and columns | matchds_1to2 |
| query_si | query_si |
| Form an RGChannelSet from a list containing signal data matrices | rgse |
| servermatrix | servermatrix |
| setup_sienv | setup_sienv |
| smfilt | smfilt |
