Package: cicero 1.23.0
cicero: Predict cis-co-accessibility from single-cell chromatin accessibility data
Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends monocle 2 for use in chromatin accessibility data.
Authors:
cicero_1.23.0.tar.gz
cicero_1.23.0.tar.gz(r-4.5-noble)cicero_1.23.0.tar.gz(r-4.4-noble)
cicero_1.23.0.tgz(r-4.4-emscripten)cicero_1.23.0.tgz(r-4.3-emscripten)
cicero.pdf |cicero.html✨
cicero/json (API)
NEWS
# Install 'cicero' in R: |
install.packages('cicero', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- cell_data - Metadata for example cells in cicero_data
- cicero_data - Example single-cell chromatin accessibility data
- gene_annotation_sample - Example gene annotation information
- human.hg19.genome - Chromosome lengths from human genome hg19
On BioConductor:cicero-1.23.0(bioc 3.20)cicero-1.22.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:c8c451922b
Exports:aggregate_by_cell_binaggregate_nearby_peaksannotate_cds_by_siteassemble_connectionsbuild_gene_activity_matrixcompare_connectionsdf_for_coordsestimate_distance_parameterfind_overlapping_ccansfind_overlapping_coordinatesgenerate_ccansgenerate_cicero_modelsmake_atac_cdsmake_cicero_cdsnormalize_gene_activitiesplot_accessibility_in_pseudotimeplot_connectionsranges_for_coordsrun_cicero
Dependencies:abindAnnotationDbiAnnotationFilteraskpassassertthatbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiocViewsbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecombinatcpp11crayoncurldata.tableDBIdbplyrDDRTreeDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastICAfastmapfilelockFNNfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2glassogluegraphgridExtragtableGvizhighrHmischmsHSMMSingleCellhtmlTablehtmltoolshtmlwidgetshttrhttr2igraphinterpIRangesirlbaisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevalleidenbaselifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemonoclemunsellnlmennetopensslpheatmappillarpkgconfigplogrplyrpngprettyunitsprogressProtGenericsproxypurrrR6RANNrappdirsRBGLRColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerRtsneRUnitS4ArraysS4VectorssassscalesslamsnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsVGAMviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc