HiCExperiment - Bioconductor class for interacting with Hi-C files in R

R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The `HiCExperiment` class stores the Hi-C contacts parsed from local contact matrix files. `HiCExperiment` instances can be further investigated in R using the `HiContacts` analysis package.

Last updated 25 days ago

hicdna3dstructuredataimport

6.94 score 9 stars 2 packages 32 scripts 256 downloads

HiContacts - Analysing cool files in R with HiContacts

HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.

Last updated 25 days ago

hicdna3dstructure

6.11 score 10 stars 43 scripts 225 downloads

tidyCoverage - Extract and aggregate genomic coverage over features of interest

`tidyCoverage` framework enables tidy manipulation of collections of genomic tracks and features using `tidySummarizedExperiment` methods. It facilitates the extraction, aggregation and visualization of genomic coverage over individual or thousands of genomic loci, relying on `CoverageExperiment` and `AggregatedCoverage` classes. This accelerates the integration of genomic track data in genomic analysis workflows.

Last updated 25 days ago

softwaresequencingcoverage

6.08 score 20 stars 6 scripts 121 downloads

VplotR - Set of tools to make V-plots and compute footprint profiles

The pattern of digestion and protection from DNA nucleases such as DNAse I, micrococcal nuclease, and Tn5 transposase can be used to infer the location of associated proteins. This package contains useful functions to analyze patterns of paired-end sequencing fragment density. VplotR facilitates the generation of V-plots and footprint profiles over single or aggregated genomic loci of interest.

Last updated 25 days ago

nucleosomepositioningcoveragesequencingbiologicalquestionatacseqalignment

5.82 score 10 stars 11 scripts 168 downloads

periodicDNA - Set of tools to identify periodic occurrences of k-mers in DNA sequences

This R package helps the user identify k-mers (e.g. di- or tri-nucleotides) present periodically in a set of genomic loci (typically regulatory elements). The functions of this package provide a straightforward approach to find periodic occurrences of k-mers in DNA sequences, such as regulatory elements. It is not aimed at identifying motifs separated by a conserved distance; for this type of analysis, please visit MEME website.

Last updated 25 days ago

sequencematchingmotifdiscoverymotifannotationsequencingcoveragealignmentdataimport

5.26 score 6 stars 4 scripts 146 downloads

BiocBook - Write, containerize, publish and version Quarto books with Bioconductor

A BiocBook can be created by authors (e.g. R developers, but also scientists, teachers, communicators, ...) who wish to 1) write (compile a body of biological and/or bioinformatics knowledge), 2) containerize (provide Docker images to reproduce the examples illustrated in the compendium), 3) publish (deploy an online book to disseminate the compendium), and 4) version (automatically generate specific online book versions and Docker images for specific Bioconductor releases).

Last updated 25 days ago

infrastructurereportwritingsoftware

4.85 score 2 stars 4 scripts 125 downloads

plyinteractions - Extending tidy verbs to genomic interactions

Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows.

Last updated 25 days ago

softwareinfrastructure

4.75 score 14 scripts 144 downloads

HiCool - HiCool

HiCool provides an R interface to process and normalize Hi-C paired-end fastq reads into .(m)cool files. .(m)cool is a compact, indexed HDF5 file format specifically tailored for efficiently storing HiC-based data. On top of processing fastq reads, HiCool provides a convenient reporting function to generate shareable reports summarizing Hi-C experiments and including quality controls.

Last updated 25 days ago

hicdna3dstructuredataimport

4.30 score 2 stars 10 scripts 148 downloads