Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
Top 0.7% on spack.io
Top 1.4% dependent packages on spack.io
Top 1.4% dependent packages on spack.io
spack.io : r-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.
Registry
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Source
- JSON
purl: pkg:spack/r-genomicranges
License: Other
Latest release: about 2 years ago
First release: about 2 years ago
Dependent packages: 46
Last synced: 9 days ago
bioconductor-tximeta 1.18.1
Transcript Quantification Import with Automatic Metadata Transcript quantification import from Sa...1 version - Latest release: 9 months ago
r-signac 1.9.0
Analysis of Single-Cell Chromatin Data. A framework for the analysis and exploration of single-ce...3 versions - Latest release: 11 months ago - 1 maintainer
r-exomedepth 1.1.16
Calls Copy Number Variants from Targeted Sequence Data. Calls copy number variants (CNVs) from ta...2 versions - Latest release: over 1 year ago - 1 maintainer
r-yapsa 1.20.1
Yet Another Package for Signature Analysis. This package provides functions and routines useful i...7 versions - Latest release: about 2 years ago - 1 maintainer
Top 4.2% on spack.io
7 versions - Latest release: about 2 years ago - 6 dependent packages - 1 maintainer
r-variantannotation 1.40.0
Annotation of Genetic Variants. Annotate variants, compute amino acid coding changes, predict cod...7 versions - Latest release: about 2 years ago - 6 dependent packages - 1 maintainer
r-tfbstools 1.32.0
Software Package for Transcription Factor Binding Site (TFBS) Analysis. TFBSTools is a package fo...7 versions - Latest release: about 2 years ago - 1 maintainer
Top 1.6% on spack.io
8 versions - Latest release: about 2 years ago - 20 dependent packages - 1 maintainer
r-summarizedexperiment 1.24.0
SummarizedExperiment container. The SummarizedExperiment container contains one or more assays, e...8 versions - Latest release: about 2 years ago - 20 dependent packages - 1 maintainer
r-somaticsignatures 2.30.0
Somatic Signatures. The SomaticSignatures package identifies mutational signatures of single nucl...7 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
Top 9.5% on spack.io
6 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-singlecellexperiment 1.16.0
S4 Classes for Single Cell Data. Defines a S4 class for storing data from single-cell experiments...6 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
Top 9.5% on spack.io
7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-shortread 1.52.0
FASTQ input and manipulation. This package implements sampling, iteration, and input of FASTQ fil...7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-scuttle 1.4.0
Single-Cell RNA-Seq Analysis Utilities. Provides basic utility functions for performing single-ce...2 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
Top 3.1% on spack.io
7 versions - Latest release: about 2 years ago - 9 dependent packages - 1 maintainer
r-rtracklayer 1.54.0
R interface to genome annotation files and the UCSC genome browser. Extensible framework for inte...7 versions - Latest release: about 2 years ago - 9 dependent packages - 1 maintainer
Top 1.6% on spack.io
8 versions - Latest release: about 2 years ago - 19 dependent packages - 1 maintainer
r-rsamtools 2.10.0
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import. This package provides a...8 versions - Latest release: about 2 years ago - 19 dependent packages - 1 maintainer
r-rnaseqmap 2.48.0
rnaSeq secondary analyses. The rnaSeqMap library provides classes and functions to analyze the RN...6 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
r-organismdbi 1.36.0
Software to enable the smooth interfacing of different database packages. The package enables a s...7 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
r-oligoclasses 1.56.0
Classes for high-throughput arrays supported by oligo and crlmm. This package contains class defi...7 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
Top 9.5% on spack.io
2 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-missmethyl 1.28.0
Analysing Illumina HumanMethylation BeadChip Data. Normalisation, testing for differential variab...2 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
Top 3.1% on spack.io
7 versions - Latest release: about 2 years ago - 9 dependent packages - 1 maintainer
r-minfi 1.40.0
Analyze Illumina Infinium DNA methylation arrays. Tools to analyze & visualize Illumina Infinium ...7 versions - Latest release: about 2 years ago - 9 dependent packages - 1 maintainer
Top 7.1% on spack.io
3 versions - Latest release: about 2 years ago - 3 dependent packages - 1 maintainer
r-methylumi 2.40.1
Handle Illumina methylation data. This package provides classes for holding and manipulating Illu...3 versions - Latest release: about 2 years ago - 3 dependent packages - 1 maintainer
r-lumi 2.46.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays. The lumi package ...3 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
Top 9.5% on spack.io
7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-gviz 1.38.3
Plotting data and annotation information along genomic coordinates. Genomic data analyses require...7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-gtrellis 1.26.0
Genome Level Trellis Layout. Genome level Trellis graph visualizes genomic data conditioned by ge...7 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
r-gofuncr 1.14.0
Gene ontology enrichment using FUNC. GOfuncR performs a gene ontology enrichment analysis based o...5 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
Top 9.5% on spack.io
7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-ggbio 1.42.0
Visualization tools for genomic data. The ggbio package extends and specializes the grammar of gr...7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
Top 1.8% on spack.io
7 versions - Latest release: about 2 years ago - 17 dependent packages - 1 maintainer
r-genomicfeatures 1.46.4
Conveniently import and query gene models. A set of tools and methods for making and manipulating...7 versions - Latest release: about 2 years ago - 17 dependent packages - 1 maintainer
Top 2.5% on spack.io
7 versions - Latest release: about 2 years ago - 11 dependent packages - 1 maintainer
r-genomicalignments 1.30.0
Representation and manipulation of short genomic alignments. Provides efficient containers for st...7 versions - Latest release: about 2 years ago - 11 dependent packages - 1 maintainer
r-exomecopy 1.40.0
Copy number variant detection from exome sequencing read depth. Detection of copy number variants...3 versions - Latest release: about 2 years ago - 1 maintainer
Top 7.1% on spack.io
7 versions - Latest release: about 2 years ago - 4 dependent packages - 1 maintainer
r-ensembldb 2.18.3
Utilities to create and use Ensembl-based annotation databases. The package provides functions to...7 versions - Latest release: about 2 years ago - 4 dependent packages - 1 maintainer
r-dmrcate 2.8.5
Methylation array and sequencing spatial analysis methods. De novo identification and extraction ...2 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
r-dexseq 1.40.0
Inference of differential exon usage in RNA-Seq. The package is focused on finding differential e...2 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
Top 3.8% on spack.io
7 versions - Latest release: about 2 years ago - 8 dependent packages - 1 maintainer
r-deseq2 1.34.0
Differential gene expression analysis based on the negative binomial distribution. Estimate varia...7 versions - Latest release: about 2 years ago - 8 dependent packages - 1 maintainer
r-condop 1.0
Condition-Dependent Operon Predictions. An implementation of the computational strategy for the c...1 version - Latest release: about 2 years ago - 1 maintainer
r-cner 1.30.0
CNE Detection and Visualization. Large-scale identification and advanced visualization of sets of...7 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
r-chipseq 1.44.0
A package for analyzing chipseq data, Tools for helping process short read data for chipseq exper...2 versions - Latest release: about 2 years ago - 1 maintainer
r-champdata 2.26.0
Packages for ChAMP package. Provides datasets needed for ChAMP including a test dataset and blood...2 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
r-champ 2.24.0
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC. The package include...2 versions - Latest release: about 2 years ago - 1 maintainer
Top 9.5% on spack.io
7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-bumphunter 1.36.0
Bump Hunter. Tools for finding bumps in genomic data7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
Top 9.5% on spack.io
5 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-bsseq 1.30.0
Analyze, manage and store bisulfite sequencing data. A collection of tools for analyzing and visu...5 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
Top 3.8% on spack.io
7 versions - Latest release: about 2 years ago - 7 dependent packages - 1 maintainer
r-bsgenome 1.62.0
Software infrastructure for efficient representation of full genomes and their SNPs. Infrastructu...7 versions - Latest release: about 2 years ago - 7 dependent packages - 1 maintainer
Top 9.5% on spack.io
7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-biovizbase 1.42.0
Basic graphic utilities for visualization of genomic data. The biovizBase package is designed to ...7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-bamsignals 1.26.0
Extract read count signals from bam files. This package allows to efficiently obtain count vector...7 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
Top 7.1% on spack.io
7 versions - Latest release: about 2 years ago - 3 dependent packages - 1 maintainer
r-annotationfilter 1.18.0
Facilities for Filtering Bioconductor Annotation Resources. This package provides class and other...7 versions - Latest release: about 2 years ago - 3 dependent packages - 1 maintainer
r-aneufinder 1.22.0
Analysis of Copy Number Variation in Single-Cell-Sequencing Data. AneuFinder implements functions...7 versions - Latest release: about 2 years ago - 1 maintainer
r-alpine 1.20.0
alpine. Fragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.7 versions - Latest release: about 2 years ago - 1 maintainer
r-allelicimbalance 1.32.0
Investigates Allele Specific Expression. Provides a framework for allelic specific expression inv...7 versions - Latest release: about 2 years ago - 1 maintainer
r-aldex2 1.26.0
Analysis Of Differential Abundance Taking Sample Variation Into Account. A differential abundance...7 versions - Latest release: about 2 years ago - 1 maintainer