Package: GOTHiC 1.48.0

Borbala Mifsud

GOTHiC: Binomial test for Hi-C data analysis

This is a Hi-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. It takes mapped paired NGS reads as input and gives back the list of significant interactions for a given bin size in the genome.

Authors:Borbala Mifsud and Robert Sugar

GOTHiC_1.48.0.tar.gz
GOTHiC_1.48.0.zip(r-4.7)GOTHiC_1.48.0.zip(r-4.6)GOTHiC_1.48.0.zip(r-4.5)
GOTHiC_1.48.0.tgz(r-4.6-any)GOTHiC_1.48.0.tgz(r-4.5-any)
GOTHiC_1.48.0.tar.gz(r-4.7-any)GOTHiC_1.48.0.tar.gz(r-4.6-any)
GOTHiC_1.48.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GOTHiC/json (API)

# Install 'GOTHiC' in R:

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

Datasets:

filtered - A GenomicRangesList object used as an example in the GOTHiC package

On BioConductor:GOTHiC-1.49.0(bioc 3.24)GOTHiC-1.48.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology sequencing preprocessing epigenetics hic

3.48 score 10 scripts 534 downloads 4 exports 77 dependencies

Last updated from:d9e409fed3 (on RELEASE_3_23). Checks:1 ERROR, 9 OK. Indexed: no.

Target	Result	Time
bioc-checks	ERROR	198
linux-devel-x86_64	OK	506
source / vignettes	OK	275
linux-release-x86_64	OK	475
macos-release-arm64	OK	311
macos-oldrel-arm64	OK	403
windows-devel	OK	422
windows-release	OK	428
windows-oldrel	OK	355
wasm-release	OK	145

Exports:GOTHiC GOTHiChicup mapReadsToRestrictionSites pairReads

Dependencies:abind askpass BH Biobase BiocGenerics BiocIO BiocManager BiocParallel Biostrings bitops BSgenome cigarillo cli codetools cpp11 crayon curl data.table DelayedArray deldir farver formatR futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 glue gtable httr hwriter interp IRanges isoband jpeg jsonlite labeling lambda.r lattice latticeExtra lifecycle MASS Matrix MatrixGenerics matrixStats mime openssl png pwalign R6 RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors S7 scales Seqinfo ShortRead snow SparseArray SummarizedExperiment sys vctrs viridisLite withr XML XVector yaml

GOTHiC

Rendered frompackage_vignettes.Snwusingutils::Sweaveon May 27 2026.

Last update: 2015-05-07
Started: 2013-11-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A GenomicRangesList object used as an example in the GOTHiC package	filtered lymphoid_chr20_paired_filtered
Genome Organisation Through HiC	GOTHiC
Genome Organisation Through HiC from HiCUP output	GOTHiChicup
Function to map aligned and paired reads to the restriction fragments	mapReadsToRestrictionSites
Function pairs aligned paired NGS reads	pairReads