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-any)GOTHiC_1.49.0.zip(r-4.6-any)GOTHiC_1.49.0.zip(r-4.5-any)
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

4.45 score 14 scripts 656 downloads 17 mentions 4 exports 71 dependencies

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

Target	Result	Time
bioc-checks	ERROR	187
linux-devel	NOTE	389
source / vignettes	OK	336
linux-release	OK	433
macos-release	OK	284
macos-oldrel	OK	294
windows-devel	NOTE	341
windows-release	OK	299
windows-oldrel	OK	341
wasm-release	OK	144

Exports:GOTHiC GOTHiChicup mapReadsToRestrictionSites pairReads

Dependencies:askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocManager BiocParallel Biostrings bitops BSgenome cigarillo cli codetools cpp11 crayon curl data.table 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 matrixStats mime openssl png pwalign R6 RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Vectors S7 scales Seqinfo ShortRead snow 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