Package: infercnv 1.23.0
infercnv: Infer Copy Number Variation from Single-Cell RNA-Seq Data
Using single-cell RNA-Seq expression to visualize CNV in cells.
Authors:
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infercnv.pdf |infercnv.html✨
infercnv/json (API)
NEWS
# Install 'infercnv' in R: |
install.packages('infercnv', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/broadinstitute/infercnv/issues
- HMM_states - Infercnv object result of the processing of run() in the HMM example, to be used for other examples.
- infercnv_annots_example - Generated classification for 10 normal cells and 10 tumor cells.
- infercnv_data_example - Generated SmartSeq2 expression data with 10 normal cells and 10 tumor cells. This is only to demonstrate how to use methods, not actual data to be used in an analysis.
- infercnv_genes_example - Downsampled gene coordinates file from GrCh37
- infercnv_object_example - Infercnv object result of the processing of run() in the example, to be used for other examples.
- mcmc_obj - Infercnv object result of the processing of inferCNVBayesNet in the example, to be used for other examples.
On BioConductor:infercnv-1.23.0(bioc 3.21)infercnv-1.22.0(bioc 3.20)
softwarecopynumbervariationvariantdetectionstructuralvariationgenomicvariationgeneticstranscriptomicsstatisticalmethodbayesianhiddenmarkovmodelsinglecelljagscpp
Last updated 2 months agofrom:ec059e200c. Checks:OK: 1 NOTE: 6. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 27 2024 |
R-4.5-win | NOTE | Nov 27 2024 |
R-4.5-linux | NOTE | Nov 27 2024 |
R-4.4-win | NOTE | Nov 27 2024 |
R-4.4-mac | NOTE | Nov 27 2024 |
R-4.3-win | NOTE | Nov 27 2024 |
R-4.3-mac | NOTE | Nov 27 2024 |
Exports:add_to_seuratapply_median_filteringcolor.paletteCreateInfercnvObjectfilterHighPNormalsinferCNVBayesNetplot_cnvplot_per_groupplot_subclustersrunsample_object
Dependencies:abindapeargparseaskpassbase64encBHBiobaseBiocGenericsbitopsbslibcachemcaToolscliclustercodacodetoolscoincolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydeldirdigestdoParalleldotCall64dplyrdqrngedgeRevaluatefansifarverfastclusterfastDummiesfastmapfindpythonfitdistrplusFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolshereHiddenMarkovhighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlibcoinlifecyclelimmalistenvlmtestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImodeltoolsmultcompmunsellmvtnormnlmeopensslparallelDistparallellypatchworkpbapplyphyclustpillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppParallelRcppProgressRcppTOMLreshape2reticulaterjagsrlangrmarkdownROCRrprojrootRSpectraRtsneS4ArraysS4VectorssandwichsassscalesscattermoresctransformSeuratSeuratObjectshinySingleCellExperimentsitmosourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrSummarizedExperimentsurvivalsystensorTH.datatibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlzlibbioczoo