Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
Top 0.5% on spack.io
Top 1.0% dependent packages on spack.io
Top 1.0% dependent packages on spack.io
spack.io : r-s4vectors
Foundation of vector-like and list-like containers in Bioconductor. The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list- like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).
Registry
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Source
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purl: pkg:spack/r-s4vectors
License: Other
Latest release: about 2 years ago
First release: about 2 years ago
Dependent packages: 64
Last synced: 3 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: 10 months ago - 1 maintainer
r-restfulr 0.0.15
R Interface to RESTful Web Services. Models a RESTful service as if it were a nested R list.2 versions - Latest release: over 1 year ago - 1 dependent package - 1 maintainer
Top 2.0% on spack.io
7 versions - Latest release: about 2 years ago - 14 dependent packages - 1 maintainer
r-xvector 0.34.0
Foundation of external vector representation and manipulation in Bioconductor. Provides memory ef...7 versions - Latest release: about 2 years ago - 14 dependent packages - 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
r-scater 1.22.0
Single-Cell Analysis Toolkit for Gene Expression Data in R. A collection of tools for doing vario...7 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
r-scaledmatrix 1.2.0
Creating a DelayedMatrix of Scaled and Centered Values. Provides delayed computation of a matrix ...1 version - 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-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
r-msnbase 2.20.4
Base Functions and Classes for Mass Spectrometry and Proteomics. MSnbase provides infrastructure ...7 versions - Latest release: about 2 years ago - 1 maintainer
r-mscoreutils 1.6.0
Core Utils for Mass Spectrometry Data. MsCoreUtils defines low-level functions for mass spectrome...1 version - 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
Top 0.6% on spack.io
8 versions - Latest release: about 2 years ago - 54 dependent packages - 1 maintainer
r-iranges 2.28.0
Foundation of integer range manipulation in Bioconductor. Provides efficient low-level and highly...8 versions - Latest release: about 2 years ago - 54 dependent packages - 1 maintainer
Top 5.8% on spack.io
7 versions - Latest release: about 2 years ago - 4 dependent packages - 1 maintainer
r-hdf5array 1.22.1
HDF5 backend for DelayedArray objects. Implements the HDF5Array and TENxMatrix classes, 2 conveni...7 versions - Latest release: about 2 years ago - 4 dependent packages - 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
Top 9.5% on spack.io
7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-glimma 2.4.0
Interactive HTML graphics. This package generates interactive visualisations for analysis of RNA-...7 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-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 0.7% on spack.io
7 versions - Latest release: about 2 years ago - 46 dependent packages - 1 maintainer
r-genomicranges 1.46.1
Representation and manipulation of genomic intervals. The ability to efficiently represent and ma...7 versions - Latest release: about 2 years ago - 46 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
Top 1.0% on spack.io
7 versions - Latest release: about 2 years ago - 31 dependent packages - 1 maintainer
r-genomeinfodb 1.30.1
Utilities for manipulating chromosome names, including modifying them to follow a particular nami...7 versions - Latest release: about 2 years ago - 31 dependent packages - 1 maintainer
Top 2.0% on spack.io
8 versions - Latest release: about 2 years ago - 14 dependent packages - 1 maintainer
r-genefilter 1.76.0
Methods for filtering genes from high-throughput experiments. Some basic functions for filtering ...8 versions - Latest release: about 2 years ago - 14 dependent packages - 1 maintainer
r-experimenthub 2.2.1
Client to access ExperimentHub resources. This package provides a client for the Bioconductor Exp...2 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 - 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
Top 9.5% on spack.io
7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-dose 3.20.1
Disease Ontology Semantic and Enrichment analysis. This package implements five methods proposed ...7 versions - Latest release: about 2 years ago - 2 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-dirichletmultinomial 1.36.0
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data. Dirichlet-multinomial m...7 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
Top 5.8% on spack.io
6 versions - Latest release: about 2 years ago - 4 dependent packages - 1 maintainer
r-delayedmatrixstats 1.16.0
Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects. A port of the 'matrixStats' ...6 versions - Latest release: about 2 years ago - 4 dependent packages - 1 maintainer
Top 2.4% on spack.io
7 versions - Latest release: about 2 years ago - 12 dependent packages - 1 maintainer
r-delayedarray 0.20.0
A unified framework for working transparently with on-disk and in-memory array-like datasets. Wra...7 versions - Latest release: about 2 years ago - 12 dependent packages - 1 maintainer
r-decipher 2.22.0
Tools for curating, analyzing, and manipulating biological sequences. A toolset for deciphering a...7 versions - Latest release: about 2 years ago - 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-complexheatmap 2.10.0
Make Complex Heatmaps. Complex heatmaps are efficient to visualize associations between different...7 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
r-codex 1.26.0
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing. A normaliz...3 versions - 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
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
Top 0.9% on spack.io
7 versions - Latest release: about 2 years ago - 35 dependent packages - 1 maintainer
r-biostrings 2.62.0
Efficient manipulation of biological strings. Memory efficient string containers, string matching...7 versions - Latest release: about 2 years ago - 35 dependent packages - 1 maintainer
r-biocsingular 1.10.0
Singular Value Decomposition for Bioconductor Packages. Implements exact and approximate methods ...3 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
r-biocneighbors 1.12.0
Nearest Neighbor Detection for Bioconductor Packages. Implements exact and approximate methods fo...4 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
Top 9.5% on spack.io
1 version - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-biocio 1.4.0
Standard Input and Output for Bioconductor Packages. Implements `import()` and `export()` standar...1 version - 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 - 3 dependent packages - 1 maintainer
r-annotationhub 3.2.1
Client to access AnnotationHub resources. This package provides a client for the Bioconductor Ann...7 versions - Latest release: about 2 years ago - 3 dependent packages - 1 maintainer
r-annotationforge 1.36.0
Tools for building SQLite-based annotation data packages. Provides code for generating Annotation...7 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
Top 0.7% on spack.io
7 versions - Latest release: about 2 years ago - 49 dependent packages - 1 maintainer
r-annotationdbi 1.56.2
Manipulation of SQLite-based annotations in Bioconductor. Implements a user-friendly interface fo...7 versions - Latest release: about 2 years ago - 49 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-altcdfenvs 2.56.0
alternative CDF environments (aka probeset mappings). Convenience data structures and functions t...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
r-affycoretools 1.66.0
Functions useful for those doing repetitive analyses with Affymetrix GeneChips. Various wrapper f...7 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer