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:
GOTHiC_1.43.0.tar.gz
GOTHiC_1.43.0.zip(r-4.5)GOTHiC_1.43.0.zip(r-4.4)GOTHiC_1.43.0.zip(r-4.3)
GOTHiC_1.43.0.tgz(r-4.4-any)GOTHiC_1.43.0.tgz(r-4.3-any)
GOTHiC_1.43.0.tar.gz(r-4.5-noble)GOTHiC_1.43.0.tar.gz(r-4.4-noble)
GOTHiC_1.43.0.tgz(r-4.4-emscripten)GOTHiC_1.43.0.tgz(r-4.3-emscripten)
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')) |
- filtered - A GenomicRangesList object used as an example in the GOTHiC package
On BioConductor:GOTHiC-1.43.0(bioc 3.21)GOTHiC-1.42.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologysequencingpreprocessingepigeneticshic
Last updated 2 months agofrom:fdd7c2b265. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | OK | Nov 29 2024 |
| R-4.5-linux | OK | Nov 29 2024 |
| R-4.4-win | OK | Nov 29 2024 |
| R-4.4-mac | OK | Nov 29 2024 |
| R-4.3-win | OK | Nov 29 2024 |
| R-4.3-mac | OK | Nov 29 2024 |
Exports:GOTHiCGOTHiChicupmapReadsToRestrictionSitespairReads
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitopsBSgenomeclicodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydeldirfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehttrhwriterinterpIRangesisobandjpegjsonlitelabelinglambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigpngpwalignR6RColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalesShortReadsnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc
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 |
