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.
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hicdna3dstructuredataimport
7.77 score 12 stars 5 dependents 55 scripts 472 downloadsHiContacts - 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.
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hicdna3dstructure
6.84 score 16 stars 86 scripts 550 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.
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softwareinfrastructure
5.78 score 1 dependents 20 scripts 414 downloadstidyCoverage - 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.
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softwaresequencingcoverage
5.78 score 24 stars 8 scripts 348 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.
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sequencematchingmotifdiscoverymotifannotationsequencingcoveragealignmentdataimport
5.26 score 6 stars 6 scripts 494 downloadsBiocBook - 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).
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infrastructurereportwritingsoftwarequarto
5.24 score 7 stars 7 scripts 353 downloadsHiContactsData - HiContacts companion data package
Provides a collection of Hi-C files (pairs, (m)cool and fastq). These datasets can be read into R and further investigated and visualized with the HiContacts package. Data includes yeast Hi-C data generated by the Koszul lab from the Pasteur Institute.
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experimenthubexperimentdatasequencingdatadatapkg
4.94 score 1 dependents 29 scriptsVplotR - 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.
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nucleosomepositioningcoveragesequencingbiologicalquestionatacseqalignment
4.90 score 11 stars 18 scripts 450 downloadsHiCool - 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.
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hicdna3dstructuredataimport
4.78 score 2 stars 10 scripts 244 downloadsDNAZooData - DNA Zoo data package
DNAZooData is a data package giving programmatic access to genome assemblies and Hi-C contact matrices uniformly processed by the [DNA Zoo Consortium](https://www.dnazoo.org/). The matrices are available in the multi-resolution `.hic` format. A URL to corrected genome assemblies in `.fastq` format is also provided to the end-user.
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experimentdatasequencingdatadatapkg
4.78 score 2 stars 1 dependents 8 scriptsfourDNData - 4DN data package
fourDNData is a data package giving programmatic access to Hi-C contact matrices uniformly processed by the [4DN consortium](https://www.4dnucleome.org/). The matrices are available in the multi-resolution `.mcool` format.
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experimentdatasequencingdatadatapkg
4.78 score 2 stars 1 dependents 9 scriptsOHCA - Orchestrating Hi-C analysis with Bioconductor
The primary aim of this book is to introduce the R user to Hi-C analysis. This book starts with key concepts important for the analysis of chromatin conformation capture and then presents Bioconductor tools that can be leveraged to process, analyze, explore and visualize Hi-C data.
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hicdna3dstructurefunctionalgenomicsdatapkg
4.52 score 11 stars 2 scriptsGenomicCoordinates - Enhanced string parsing for genomic coordinates
Extends string parsing capabilities for genomic coordinates, supporting various formats including comma-separated numbers, space-delimited coordinates, and automatic detection of GRanges, GPos, and GInteractions objects.
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infrastructuredatarepresentationgenomeannotation
4.48 score 2 stars 4 scripts 312 downloads