Tag: HiTC

Bioconductor – GenomicRanges

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see GenomicRanges. Representation and manipulation of genomic intervals Bioconductor version: 2.14 The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing…

Continue Reading Bioconductor – GenomicRanges

Bioconductor – rtracklayer

DOI: 10.18129/B9.bioc.rtracklayer     R interface to genome annotation files and the UCSC genome browser Bioconductor version: Release (3.6) Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may…

Continue Reading Bioconductor – rtracklayer

how to import hdf5 Hi-C data into R using HiTC package

how to import hdf5 Hi-C data into R using HiTC package 0 Hello everyone, I was trying to use HiTC software but I am not able to understand how to input my dataset. I used this command: x <- importC(con=chr9,xgi.bed=colnames(chr9),ygi.bed = rownames(chr9)) error in evaluating the argument ‘con’ in selecting…

Continue Reading how to import hdf5 Hi-C data into R using HiTC package

Bioconductor – HiTC

DOI: 10.18129/B9.bioc.HiTC     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see HiTC. High Throughput Chromosome Conformation Capture analysis Bioconductor version: 3.9 The HiTC package was developed to explore high-throughput ‘C’ data such as 5C or Hi-C. Dedicated R classes as well as…

Continue Reading Bioconductor – HiTC