Package: GOTHiC 1.43.0

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_1.43.0.tar.gz
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GOTHiC.pdf |GOTHiC.html✨
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-1.41.0(bioc 3.20)GOTHiC-1.40.0(bioc 3.19)

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

3.30 score 6 scripts 220 downloads 4 exports 87 dependencies

Last updated 23 days agofrom:fdd7c2b265. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	OK	Oct 31 2024
R-4.5-linux	OK	Oct 30 2024
R-4.4-win	OK	Oct 31 2024
R-4.4-mac	OK	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	OK	Oct 31 2024

Exports:GOTHiC GOTHiChicup mapReadsToRestrictionSites pairReads

Dependencies:abind askpass BH Biobase BiocGenerics BiocIO BiocManager BiocParallel Biostrings bitops BSgenome cli codetools colorspace cpp11 crayon curl data.table DelayedArray deldir fansi farver formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue gtable httr hwriter interp IRanges isoband jpeg jsonlite labeling lambda.r lattice latticeExtra lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig png pwalign R6 RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors scales ShortRead snow SparseArray SummarizedExperiment sys tibble UCSC.utils utf8 vctrs viridisLite withr XML XVector yaml zlibbioc

GOTHiC

Rendered frompackage_vignettes.Snwusingutils::Sweaveon Oct 30 2024.

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