Package: GOTHiC 1.49.0

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_1.49.0.tar.gz
GOTHiC_1.49.0.zip(r-4.7)GOTHiC_1.49.0.zip(r-4.6)GOTHiC_1.49.0.zip(r-4.5)
GOTHiC_1.49.0.tgz(r-4.6-any)GOTHiC_1.49.0.tgz(r-4.5-any)
GOTHiC_1.49.0.tar.gz(r-4.7-any)GOTHiC_1.49.0.tar.gz(r-4.6-any)
GOTHiC_1.49.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GOTHiC/json (API)

# Install 'GOTHiC' in R:

install.packages('GOTHiC', repos = c('https://bioc.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

4.48 score 10 scripts 17 mentions 4 exports 78 dependencies

Last updated from:1500c83423. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	220
linux-devel-x86_64	WARNING	481
source / vignettes	OK	267
linux-release-x86_64	WARNING	541
macos-release-arm64	WARNING	406
macos-oldrel-arm64	WARNING	376
windows-devel	WARNING	385
windows-release	WARNING	382
windows-oldrel	WARNING	412
wasm-release	OK	188

Exports:GOTHiC GOTHiChicup mapReadsToRestrictionSites pairReads

Dependencies:abind askpass BH Biobase BiocBaseUtils 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::Sweave

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