dichromat: stats IRanges: methods utils stats BiocGenerics S4Vectors stats4 R.methodsS3: utils drosophila2probe: AnnotationDbi progress: crayon hms prettyunits R6 vsn: methods Biobase affy limma lattice ggplot2 nnet: stats utils BSgenome.Celegans.UCSC.ce2: BSgenome Biostrings: BiocGenerics S4Vectors IRanges XVector GenomeInfoDb methods utils grDevices stats crayon affyPLM: BiocGenerics affy Biobase gcrma stats preprocessCore graphics grDevices methods HDF5Array: methods SparseArray DelayedArray h5mread utils stats tools Matrix BiocGenerics S4Vectors IRanges S4Arrays rhdf5 EnsDb.Hsapiens.v75: ensembldb TxDb.Hsapiens.UCSC.hg38.knownGene: GenomicFeatures AnnotationDbi vctrs: cli glue lifecycle rlang digest: utils png: MSnbase: methods BiocGenerics Biobase mzR S4Vectors ProtGenerics MsCoreUtils PSMatch BiocParallel IRanges plyr vsn grid stats4 affy impute pcaMethods MALDIquant mzID digest lattice ggplot2 scales MASS Rcpp BiocBaseUtils: methods utils deldir: graphics grDevices Rattus.norvegicus: AnnotationDbi methods OrganismDbi GenomicFeatures GO.db org.Rn.eg.db TxDb.Rnorvegicus.UCSC.rn5.refGene MASS: grDevices graphics stats utils methods reshape2: plyr Rcpp stringr RcppArmadillo: Rcpp stats utils methods foreach: codetools utils iterators TxDb.Dmelanogaster.UCSC.dm3.ensGene: GenomicFeatures AnnotationDbi BiocGenerics: methods utils graphics stats generics withr: graphics grDevices xfun: grDevices stats tools MetaboCoreUtils: utils MsCoreUtils BiocParallel methods stats survival: graphics Matrix methods splines stats utils memoise: rlang cachem utils: RProtoBufLib: KEGGgraph: methods XML graph utils RCurl Rgraphviz R.oo: R.methodsS3 methods utils sys: Formula: stats prettyunits: promises: fastmap later magrittr R6 Rcpp rlang stats KEGGREST: methods httr png Biostrings RMariaDB: bit64 blob DBI hms lubridate methods rlang cpp11 plogr hgu95av2: httr: curl jsonlite mime openssl R6 restfulr: methods XML RCurl rjson S4Vectors yaml rhdf5filters: Rhdf5lib rstudioapi: ps: utils rhdf5: methods Rhdf5lib rhdf5filters UCSC.utils: methods stats httr jsonlite S4Vectors generics: methods reactome.db: methods AnnotationDbi base64enc: processx: ps R6 utils curl: ncdf4: S4Vectors: methods utils stats stats4 BiocGenerics h5mread: methods rhdf5 BiocGenerics SparseArray stats tools rhdf5filters S4Vectors IRanges S4Arrays Rhdf5lib GenomeInfoDbData: SparseArray: methods Matrix BiocGenerics MatrixGenerics S4Vectors S4Arrays utils stats matrixStats IRanges XVector RcppEigen: Rcpp stats utils RBGL: graph methods BH doParallel: foreach iterators parallel utils xtable: stats utils stringr: cli glue lifecycle magrittr rlang stringi vctrs desc: cli R6 utils evaluate: S4Arrays: methods Matrix abind BiocGenerics S4Vectors IRanges stats crayon flowClust: BiocGenerics methods Biobase graph flowCore parallel BiocFileCache: dbplyr methods stats utils dplyr RSQLite DBI filelock curl httr2 preprocessCore: stats hms: lifecycle methods pkgconfig rlang vctrs GenomicRanges: methods stats4 BiocGenerics S4Vectors IRanges GenomeInfoDb utils stats XVector bookdown: htmltools knitr rmarkdown jquerylib xfun tinytex yaml colorspace: methods graphics grDevices stats praise: filelock: isoband: grid utils org.Sc.sgd.db: methods AnnotationDbi graphics: grDevices magrittr: Rgraphviz: methods utils graph grid stats4 graphics grDevices later: Rcpp rlang viridis: viridisLite ggplot2 gridExtra SPIA: graphics KEGGgraph lattice: grid grDevices graphics stats utils widgetTools: methods utils tcltk MsCoreUtils: methods S4Vectors MASS stats clue Rcpp genefilter: MatrixGenerics AnnotationDbi annotate Biobase graphics methods stats survival grDevices cpp11: methods: utils stats org.At.tair.db: methods AnnotationDbi XML: methods utils matrixStats: Rhtslib: tools Hmisc: methods ggplot2 cluster rpart nnet foreign gtable grid gridExtra data.table htmlTable viridis htmltools base64enc colorspace rmarkdown knitr Formula pillar: cli glue lifecycle rlang utf8 utils vctrs nlme: graphics stats utils lattice iterators: utils pwalign: BiocGenerics S4Vectors IRanges Biostrings methods utils XVector compiler: stringi: tools utils stats hgu133aprobe: AnnotationDbi stats: utils grDevices graphics SummarizedExperiment: methods MatrixGenerics GenomicRanges Biobase utils stats tools Matrix BiocGenerics S4Vectors IRanges GenomeInfoDb S4Arrays DelayedArray lubridate: methods generics timechange GenomicAlignments: methods BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges SummarizedExperiment Biostrings Rsamtools utils stats BiocParallel plyr: Rcpp diffobj: crayon tools methods utils stats crayon: grDevices methods utils abind: methods utils BiocIO: BiocGenerics S4Vectors methods tools gcrma: affy graphics methods stats utils Biobase affyio XVector Biostrings splines BiocManager locfit: lattice plogr: org.Hs.eg.db: methods AnnotationDbi bit: waldo: cli diffobj glue methods rlang DynDoc: methods utils pcaMethods: Biobase methods BiocGenerics Rcpp MASS dplyr: cli generics glue lifecycle magrittr methods pillar R6 rlang tibble tidyselect utils vctrs codetools: TxDb.Mmusculus.UCSC.mm10.knownGene: GenomicFeatures AnnotationDbi openssl: askpass crosstalk: htmltools jsonlite lazyeval R6 bslib: base64enc cachem fastmap grDevices htmltools jquerylib jsonlite lifecycle memoise mime rlang sass TxDb.Hsapiens.UCSC.hg19.knownGene: GenomicFeatures AnnotationDbi biovizBase: methods grDevices stats scales Hmisc RColorBrewer dichromat BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges SummarizedExperiment Biostrings Rsamtools GenomicAlignments GenomicFeatures AnnotationDbi VariantAnnotation ensembldb AnnotationFilter rlang plotly: ggplot2 tools scales httr jsonlite magrittr digest viridisLite base64enc htmltools htmlwidgets tidyr RColorBrewer dplyr vctrs tibble lazyeval rlang crosstalk purrr data.table promises hgu133plus2.db: methods AnnotationDbi org.Hs.eg.db DEXSeq: BiocParallel Biobase SummarizedExperiment IRanges GenomicRanges DESeq2 AnnotationDbi RColorBrewer S4Vectors BiocGenerics biomaRt hwriter methods stringr Rsamtools statmod geneplotter genefilter mime: tools org.Rn.eg.db: methods AnnotationDbi MultiAssayExperiment: SummarizedExperiment Biobase BiocBaseUtils BiocGenerics DelayedArray GenomicRanges IRanges MatrixGenerics methods S4Vectors tidyr utils splines: graphics stats Rcpp: methods utils dbplyr: blob cli DBI dplyr glue lifecycle magrittr methods pillar purrr R6 rlang tibble tidyr tidyselect utils vctrs withr interp: Rcpp deldir RcppEigen utf8: knitr: evaluate highr methods tools xfun yaml blob: methods rlang vctrs clue: stats cluster graphics methods BiocVersion: BSgenome.Hsapiens.NCBI.GRCh38: BSgenome mzR: Rcpp methods utils Biobase BiocGenerics ProtGenerics ncdf4 Rhdf5lib AnnotationFilter: utils methods GenomicRanges lazyeval fs: methods checkmate: backports utils QFeatures: MultiAssayExperiment methods stats utils S4Vectors IRanges SummarizedExperiment BiocGenerics ProtGenerics AnnotationFilter lazyeval Biobase MsCoreUtils igraph grDevices plotly tidyr tidyselect reshape2 mzID: methods XML plyr parallel doParallel foreach iterators ProtGenerics Homo.sapiens: AnnotationDbi methods OrganismDbi GenomicFeatures GO.db org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene pkgbuild: callr cli desc processx R6 Gviz: methods S4Vectors IRanges GenomicRanges grid XVector rtracklayer lattice RColorBrewer biomaRt AnnotationDbi Biobase GenomicFeatures ensembldb BSgenome Biostrings biovizBase Rsamtools latticeExtra matrixStats GenomicAlignments GenomeInfoDb BiocGenerics digest graphics grDevices stats utils tibble: fansi lifecycle magrittr methods pillar pkgconfig rlang utils vctrs Matrix: methods grDevices graphics grid lattice stats utils TxDb.Athaliana.BioMart.plantsmart22: GenomicFeatures AnnotationDbi callr: processx R6 utils statmod: stats graphics BSgenome.Hsapiens.UCSC.hg18: BSgenome pkgconfig: utils BSgenome.Hsapiens.UCSC.hg19: BSgenome tools: cachem: rlang fastmap BSgenome.Mmusculus.UCSC.mm10: BSgenome RSQLite: bit64 blob DBI memoise methods pkgconfig rlang plogr cpp11 viridisLite: DBI: methods impute: fastmap: rmarkdown: bslib evaluate fontawesome htmltools jquerylib jsonlite knitr methods tinytex tools utils xfun yaml scales: cli farver glue labeling lifecycle R6 RColorBrewer rlang viridisLite grid: grDevices utils geneplotter: methods Biobase BiocGenerics lattice annotate AnnotationDbi graphics grDevices grid RColorBrewer stats utils hgu95av2probe: AnnotationDbi Rsamtools: methods GenomeInfoDb GenomicRanges Biostrings utils BiocGenerics S4Vectors IRanges XVector bitops BiocParallel stats Rhtslib AnnotationHub: BiocGenerics BiocFileCache utils methods grDevices RSQLite BiocManager BiocVersion curl rappdirs AnnotationDbi S4Vectors httr2 yaml dplyr sass: fs rlang htmltools R6 rappdirs BSgenome.Scerevisiae.UCSC.sacCer2: BSgenome BiocManager: utils BSgenome.Dmelanogaster.UCSC.dm3: BSgenome VariantAnnotation: methods BiocGenerics MatrixGenerics GenomeInfoDb GenomicRanges SummarizedExperiment Rsamtools utils DBI Biobase S4Vectors IRanges XVector Biostrings AnnotationDbi rtracklayer BSgenome GenomicFeatures Rhtslib graph: methods BiocGenerics stats stats4 utils rpart: graphics stats grDevices fontawesome: rlang htmltools snow: utils farver: mgcv: nlme methods stats graphics Matrix splines utils yaml: AnnotationForge: methods utils BiocGenerics Biobase AnnotationDbi DBI RSQLite XML S4Vectors RCurl foreign: methods utils stats latticeExtra: lattice grid stats utils grDevices png jpeg RColorBrewer interp MASS MatrixGenerics: matrixStats methods rtracklayer: methods GenomicRanges XML BiocGenerics S4Vectors IRanges XVector GenomeInfoDb Biostrings curl httr Rsamtools GenomicAlignments BiocIO tools restfulr cli: utils purrr: cli lifecycle magrittr rlang vctrs stats4: graphics methods stats txdbmaker: BiocGenerics S4Vectors GenomeInfoDb GenomicRanges GenomicFeatures methods utils stats tools httr rjson DBI RSQLite IRanges UCSC.utils AnnotationDbi Biobase BiocIO rtracklayer biomaRt lifecycle: cli glue rlang askpass: sys Biobase: BiocGenerics utils methods backports: lambda.r: formatR golubEsets: Biobase BSgenome.Hsapiens.UCSC.hg38: GenomeInfoDb BSgenome BiocParallel: methods stats utils futile.logger parallel snow codetools BH cpp11 cytolib: RProtoBufLib BH Rhdf5lib annotate: AnnotationDbi XML Biobase DBI xtable graphics utils stats methods BiocGenerics httr gtable: cli glue grid lifecycle rlang stats timechange: cpp11 rjson: tkWidgets: methods widgetTools DynDoc tools parallel: tools compiler testthat: brio callr cli desc digest evaluate jsonlite lifecycle magrittr methods pkgload praise processx ps R6 rlang utils waldo withr limma: grDevices graphics stats utils methods statmod jsonlite: methods rex: lazyeval edgeR: limma methods graphics stats utils locfit bitops: ggplot2: cli glue grDevices grid gtable isoband lifecycle MASS mgcv rlang scales stats tibble vctrs withr bit64: bit graphics methods stats utils brio: flowCore: Biobase BiocGenerics grDevices graphics methods stats utils stats4 Rcpp matrixStats cytolib S4Vectors cpp11 BH RProtoBufLib futile.options: jquerylib: htmltools highr: xfun R.utils: R.oo methods utils tools R.methodsS3 FDb.UCSC.tRNAs: GenomicFeatures AnnotationDbi lazyeval: htmltools: base64enc digest fastmap grDevices rlang utils affy: BiocGenerics Biobase affyio BiocManager graphics grDevices methods preprocessCore stats utils GO.db: methods AnnotationDbi formatR: rappdirs: ensembldb: BiocGenerics GenomicRanges GenomicFeatures AnnotationFilter methods RSQLite DBI Biobase GenomeInfoDb AnnotationDbi rtracklayer S4Vectors Rsamtools IRanges ProtGenerics Biostrings curl tinytex: xfun glue: methods human.db0: methods AnnotationDbi tcltk: utils httr2: cli curl glue lifecycle magrittr openssl R6 rappdirs rlang vctrs withr XVector: methods BiocGenerics S4Vectors IRanges utils tools RCurl: methods bitops rprojroot: MALDIquant: methods parallel BH: BSgenome: methods BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges Biostrings BiocIO rtracklayer utils stats matrixStats XVector Rsamtools hgu95av2.db: methods AnnotationDbi org.Hs.eg.db gridExtra: gtable grid grDevices graphics utils jpeg: futile.logger: utils lambda.r futile.options igraph: methods cli graphics grDevices lifecycle magrittr Matrix pkgconfig rlang stats utils vctrs cpp11 R6: tidyr: cli dplyr glue lifecycle magrittr purrr rlang stringr tibble tidyselect utils vctrs cpp11 DESeq2: S4Vectors IRanges GenomicRanges SummarizedExperiment BiocGenerics Biobase BiocParallel matrixStats methods stats4 locfit ggplot2 Rcpp MatrixGenerics RcppArmadillo labeling: stats graphics hgu95av2cdf: utils AnnotationDbi GenomicFeatures: BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges AnnotationDbi methods utils stats DBI XVector Biostrings rtracklayer cluster: graphics grDevices stats utils pkgload: cli desc fs glue lifecycle methods pkgbuild processx rlang rprojroot utils withr Rhdf5lib: Spectra: S4Vectors BiocParallel ProtGenerics methods IRanges MsCoreUtils graphics grDevices stats tools utils fs BiocGenerics MetaboCoreUtils GenomeInfoDb: methods BiocGenerics S4Vectors IRanges stats stats4 utils UCSC.utils DelayedArray: methods stats4 Matrix BiocGenerics MatrixGenerics S4Vectors IRanges S4Arrays SparseArray stats tidyselect: cli glue lifecycle rlang vctrs withr covr: methods digest stats utils jsonlite rex httr crayon withr yaml ProtGenerics: methods htmlTable: stringr knitr magrittr methods checkmate htmlwidgets htmltools rstudioapi xml2: cli methods rlang AnnotationDbi: methods stats4 BiocGenerics Biobase IRanges DBI RSQLite S4Vectors stats KEGGREST BiocStyle: bookdown knitr rmarkdown stats utils yaml BiocManager affyio: methods data.table: methods grDevices: htmlwidgets: grDevices htmltools jsonlite knitr rmarkdown yaml ALL: Biobase RColorBrewer: hwriter: biomaRt: methods utils AnnotationDbi progress stringr httr2 digest BiocFileCache rappdirs xml2 curl rlang: utils RNAseqData.HNRNPC.bam.chr14: ShortRead: BiocGenerics BiocParallel Biostrings Rsamtools GenomicAlignments Biobase S4Vectors IRanges GenomeInfoDb GenomicRanges pwalign hwriter methods lattice latticeExtra XVector Rhtslib fansi: grDevices utils RUnit: utils methods graphics OrganismDbi: BiocGenerics AnnotationDbi GenomicFeatures methods utils stats DBI BiocManager Biobase graph RBGL S4Vectors IRanges GenomicRanges txdbmaker pasillaBamSubset: TxDb.Rnorvegicus.UCSC.rn5.refGene: GenomicFeatures AnnotationDbi PSMatch: S4Vectors utils stats igraph methods Spectra Matrix BiocParallel BiocGenerics ProtGenerics QFeatures MsCoreUtils IRanges affydata: affy methods