Showing 10 of total 10 results (show query)
bioc
GenomicRanges:Representation and manipulation of genomic intervals
The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.
Maintained by Hervé Pagès. Last updated 5 months ago.
geneticsinfrastructuredatarepresentationsequencingannotationgenomeannotationcoveragebioconductor-packagecore-package
44 stars 17.68 score 13k scripts 1.3k dependentsbioc
SummarizedExperiment:A container (S4 class) for matrix-like assays
The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.
Maintained by Hervé Pagès. Last updated 5 months ago.
geneticsinfrastructuresequencingannotationcoveragegenomeannotationbioconductor-packagecore-package
34 stars 16.84 score 8.6k scripts 1.2k dependentsbioc
IRanges:Foundation of integer range manipulation in Bioconductor
Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.
Maintained by Hervé Pagès. Last updated 2 months ago.
infrastructuredatarepresentationbioconductor-packagecore-package
22 stars 16.09 score 2.1k scripts 1.8k dependentsbioc
GenomicAlignments:Representation and manipulation of short genomic alignments
Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.
Maintained by Hervé Pagès. Last updated 5 months ago.
infrastructuredataimportgeneticssequencingrnaseqsnpcoveragealignmentimmunooncologybioconductor-packagecore-package
10 stars 15.21 score 3.1k scripts 528 dependentsbioc
bsseq:Analyze, manage and store whole-genome methylation data
A collection of tools for analyzing and visualizing whole-genome methylation data from sequencing. This includes whole-genome bisulfite sequencing and Oxford nanopore data.
Maintained by Kasper Daniel Hansen. Last updated 4 months ago.
37 stars 12.26 score 676 scripts 15 dependents
stuart-lab
Signac:Analysis of Single-Cell Chromatin Data
A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.
Maintained by Tim Stuart. Last updated 7 months ago.
atacbioinformaticssingle-cellzlibcpp
355 stars 12.18 score 3.7k scripts 1 dependentsbioc
InteractionSet:Base Classes for Storing Genomic Interaction Data
Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.
Maintained by Aaron Lun. Last updated 5 months ago.
infrastructuredatarepresentationsoftwarehiccpp
7.95 score 250 scripts 36 dependentsbioc
DEXSeq:Inference of differential exon usage in RNA-Seq
The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.
Maintained by Alejandro Reyes. Last updated 1 months ago.
immunooncologysequencingrnaseqdifferentialexpressionalternativesplicingdifferentialsplicinggeneexpressionvisualization
7.75 score 330 scripts 6 dependentsbioc
oligoClasses:Classes for high-throughput arrays supported by oligo and crlmm
This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.
Maintained by Benilton Carvalho. Last updated 5 months ago.
5.86 score 93 scripts 17 dependentsbioc
GenomicTuples:Representation and Manipulation of Genomic Tuples
GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package.
Maintained by Peter Hickey. Last updated 5 months ago.
infrastructuredatarepresentationsequencingcpp
4 stars 5.48 score 7 scripts