Package: CNVMotif 0.1.0
CNVMotif: Explore, Analyze and Visualize Catalogs and Patterns of Copy Number Variation in Cancer Genomics
Provides functionality for exploring, analyzing and visualizing the copy number variation (CNV) motifs in cancer genomics.
Authors:
CNVMotif_0.1.0.tar.gz
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CNVMotif.pdf |CNVMotif.html✨
CNVMotif/json (API)
| # Install 'CNVMotif' in R: |
| install.packages('CNVMotif', repos = c('https://shixiangwang.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/shixiangwang/cnvmotif/issues
Last updated 2 years agofrom:ad11585b11
Exports:%>%build_sub_matrixcluster_pamcluster_pam_estimatecluster_splitdo_msaextract_seqsgeom_logo2get_score_matrixggseqlogo2show_seq_logoshow_seq_shapetransform_seqs
Dependencies:abindaskpassbackportsbase64encBiocGenericsBiostringsbootbroombslibcachemcarcarDatacliclustercolorspacecorrplotcowplotcpp11crayoncrosstalkcurldata.tabledendextendDerivdigestdoBydplyrDTellipseemmeansestimabilityevaluatefactoextraFactoMineRfansifarverfastmapflashClustfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataggplot2ggpubrggrepelggsciggseqlogoggsignifgluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevalleapslifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamodelrmsamultcompViewmunsellmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplyrpolynompromisespurrrquantregR6rappdirsRColorBrewerRcppRcppEigenreshape2rlangrmarkdownrstatixS4Vectorssassscalesscatterplot3dSparseMstringistringrsurvivalsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisviridisLitewithrxfunXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Build a Substitution Matrix | build_sub_matrix |
| Estimate Optimal Number of Cluster for PAM Algorithm | cluster_pam cluster_pam_estimate |
| Split Cluster Sequence into List | cluster_split |
| Run Modified Multiple Sequence Alignment | do_msa |
| Extract Pasted Sequences from Each Chromosome | extract_seqs |
| Get Copy Number Sequence Similarity or Distance Matrix | get_score_matrix |
| Quick sequence logo plot | geom_logo2 ggseqlogo2 |
| Show Copy Number Sequence Logos | show_seq_logo |
| Show Copy Number Sequence Shapes | show_seq_shape |
| Coding Copy Number Segments with Letters. | transform_seqs |
