Package: OHCA 1.9.2

Jacques Serizay

OHCA: Orchestrating Hi-C analysis with Bioconductor

The primary aim of this book is to introduce the R user to Hi-C analysis. This book starts with key concepts important for the analysis of chromatin conformation capture and then presents Bioconductor tools that can be leveraged to process, analyze, explore and visualize Hi-C data.

Authors:Jacques Serizay [aut, cre]

OHCA_1.9.2.tar.gz
OHCA_1.9.2.tar.gz(r-4.7-any)OHCA_1.9.2.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
OHCA/json (API)

# Install 'OHCA' in R:

install.packages('OHCA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/js2264/ohca/issues

On CRAN:

hic dna3dstructure functionalgenomics datapkg

4.52 score 11 stars 2 scripts 0 exports 204 dependencies

Last updated from:8ef6242d33. Checks:1 ERROR, 2 NOTE, 1 OK. Indexed: yes.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	ERROR	285
linux-devel	NOTE	402
source / vignettes	OK	1950
linux-release	NOTE	369

Exports:

Dependencies:abind AnnotationDbi AnnotationFilter AnnotationHub askpass backports base64enc beeswarm BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel BiocStyle BiocVersion biomaRt Biostrings biovizBase bit bit64 bitops blob bookdown BSgenome BSgenome.Hsapiens.UCSC.hg38 bslib cachem Cairo checkmate cigarillo cli clipr cluster codetools colorspace cowplot cpp11 crayon csaw curl data.table DBI dbplyr DelayedArray deldir dichromat diffHic digest dir.expiry DNAZooData doParallel dplyr dynamicTreeCut edgeR ensembldb evaluate ExperimentHub farver fastcluster fastmap filelock fontawesome foreach foreign formatR Formula fourDNData fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicInteractions GenomicRanges ggbeeswarm ggplot2 ggrastr glue GOTHiC gridExtra gtable Gviz HiCExperiment HiContacts HiContactsData highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 hwriter igraph impute InteractionSet interp IRanges isoband iterators jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise metapod mime nnet openssl pillar pkgconfig plyinteractions plyr plyranges png preprocessCore prettyunits progress ProtGenerics purrr pwalign R6 ragg rappdirs RColorBrewer Rcpp RcppEigen RCurl readr reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rpart Rsamtools RSpectra RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo sessioninfo ShortRead snow SparseArray statmod strawr stringi stringr SummarizedExperiment survival sys systemfonts textshaping tibble tidyr tidyselect tinytex TopDom tzdb UCSC.utils utf8 VariantAnnotation vctrs vipor viridisLite vroom WGCNA withr xfun XML xml2 XVector yaml

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OHCA

Rendered fromstub.Rmdusingknitr::rmarkdown

Last update: 2024-01-22
Started: 2023-11-03

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