Package: cinaR 0.2.4

Onur Karakaslar

cinaR: A Computational Pipeline for Bulk 'ATAC-Seq' Profiles

Differential analyses and Enrichment pipeline for bulk 'ATAC-seq' data analyses. This package combines different packages to have an ultimate package for both data analyses and visualization of 'ATAC-seq' data. Methods are described in 'Karakaslar et al.' (2021) <doi:10.1101/2021.03.05.434143>.

Authors:Onur Karakaslar [aut, cre], Duygu Ucar [aut]

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Bug tracker:https://github.com/eonurk/cinar/issues

On CRAN:

atac-seqdifferential-analysisenrichment-analysisgene-sets

14 exports 12 stars 1.65 score 100 dependencies 49 scripts 249 downloads

Last updated 4 months agofrom:ff44a57de4. Checks:OK: 4 ERROR: 1 NOTE: 2. Indexed: yes.

Exports:cinaRcolor_valuesdot_plotfilterConsensusGSEAheatmap_differentialheatmap_var_peaksHPEAnormalizeConsensuspca_plotrun_enrichmentscale_rowsshow_comparisonsverboseFn

Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocManagerBiocParallelBiostringsbitbit64blobcachemclicodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIDelayedArrayDESeq2dplyredgeRfansifarverfastmapfastmatchfgseaformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpheatmappillarpkgconfigplogrpngpreprocessCoreR6RColorBrewerRcppRcppArmadillorlangRSQLiteS4ArraysS4VectorsscalessnowSparseArraystatmodSummarizedExperimentsurvivalsvasystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrwritexlXMLxtableXVectorzlibbioc