Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
Top 0.3% on spack.io
Top 0.6% dependent packages on spack.io
Top 0.6% dependent packages on spack.io
spack.io : r-biocgenerics
S4 generic functions used in Bioconductor. The package defines S4 generic functions used in Bioconductor.
Registry
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Source
- JSON
purl: pkg:spack/r-biocgenerics
License: Other
Latest release: about 2 years ago
First release: about 2 years ago
Dependent packages: 78
Last synced: 4 days ago
homer 4.11.1
Software for motif discovery and next generation sequencing analysis2 versions - Latest release: 10 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-dada2 1.20
Accurate sample inference from amplicon data with single nucleotide resolution2 versions - Latest release: almost 2 years ago - 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
r-xde 2.40.0
a Bayesian hierarchical model for cross-study analysis of differential gene expression. Multi-lev...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-topgo 2.46.0
Enrichment Analysis for Gene Ontology. topGO package provides tools for testing GO terms while ac...7 versions - Latest release: about 2 years ago - 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-snpstats 1.44.0
SnpMatrix and XSnpMatrix classes and methods. Classes and statistical methods for large SNP assoc...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
6 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-simpleaffy 2.66.0
Very simple high level analysis of Affymetrix data. Provides high level functions for reading Aff...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
Top 0.5% on spack.io
8 versions - Latest release: about 2 years ago - 64 dependent packages - 1 maintainer
r-s4vectors 0.32.3
Foundation of vector-like and list-like containers in Bioconductor. The S4Vectors package defines...8 versions - Latest release: about 2 years ago - 64 dependent packages - 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-reportingtools 2.34.0
Tools for making reports in various formats. The ReportingTools software package enables users to...7 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
r-phyloseq 1.38.0
Handling and analysis of high-throughput microbiome census data. phyloseq provides a set of class...7 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-pcamethods 1.86.0
A collection of PCA methods. Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Li...7 versions - Latest release: about 2 years ago - 2 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-mzr 2.28.0
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data). mzR provi...7 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 - 7 dependent packages - 1 maintainer
r-multtest 2.50.0
Resampling-based multiple hypothesis testing. Non-parametric bootstrap and permutation resampling...7 versions - Latest release: about 2 years ago - 7 dependent packages - 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-mlinterfaces 1.74.0
Uniform interfaces to R machine learning procedures for data in Bioconductor containers. This pac...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
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
r-interactivedisplaybase 1.32.0
Base package for enabling powerful shiny web displays of Bioconductor objects. The interactiveDis...7 versions - Latest release: about 2 years ago - 1 dependent package - 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 7.1% on spack.io
7 versions - Latest release: about 2 years ago - 3 dependent packages - 1 maintainer
r-gseabase 1.56.0
Gene set enrichment data structures and methods. This package provides classes and methods to sup...7 versions - Latest release: about 2 years ago - 3 dependent packages - 1 maintainer
Top 2.2% on spack.io
7 versions - Latest release: about 2 years ago - 13 dependent packages - 1 maintainer
r-graph 1.72.0
A package to handle graph data structures. A package that implements some simple graph handling c...7 versions - Latest release: about 2 years ago - 13 dependent packages - 1 maintainer
Top 9.5% on spack.io
7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-goseq 1.46.0
Gene Ontology analyser for RNA-seq and other length biased data. Detects Gene Ontology and/or oth...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 7.1% on spack.io
7 versions - Latest release: about 2 years ago - 3 dependent packages - 1 maintainer
r-geneplotter 1.72.0
Graphics related functions for Bioconductor. Functions for plotting genomic data.7 versions - Latest release: about 2 years ago - 3 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
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 7.1% on spack.io
6 versions - Latest release: about 2 years ago - 3 dependent packages - 1 maintainer
r-deseq 1.42.0
Differential gene expression analysis based on the negative binomial distribution. Estimate varia...6 versions - Latest release: about 2 years ago - 3 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-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
Top 9.5% on spack.io
7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-category 2.60.0
Category Analysis. A collection of tools for performing category (gene set enrichment) analysis.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-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 0.3% on spack.io
7 versions - Latest release: about 2 years ago - 77 dependent packages - 1 maintainer
r-biobase 2.54.0
Biobase: Base functions for Bioconductor. Functions that are needed by many other packages or whi...7 versions - Latest release: about 2 years ago - 77 dependent packages - 1 maintainer
Top 5.8% on spack.io
6 versions - Latest release: about 2 years ago - 4 dependent packages - 1 maintainer
r-beachmat 2.10.0
Compiling Bioconductor to Handle Each Matrix Type. Provides a consistent C++ class interface for ...6 versions - Latest release: about 2 years ago - 4 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 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
Top 2.5% on spack.io
7 versions - Latest release: about 2 years ago - 11 dependent packages - 1 maintainer
r-annotate 1.72.0
Annotation for microarrays. Using R enviroments for annotation.7 versions - Latest release: about 2 years ago - 11 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-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-affyplm 1.70.0
Methods for fitting probe-level models. A package that extends and improves the functionality of ...7 versions - Latest release: about 2 years ago - 1 dependent package - 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
Top 1.7% on spack.io
7 versions - Latest release: about 2 years ago - 17 dependent packages - 1 maintainer
r-affy 1.72.0
Methods for Affymetrix Oligonucleotide Arrays. The package contains functions for exploratory oli...7 versions - Latest release: about 2 years ago - 17 dependent packages - 1 maintainer
r-acme 2.50.0
Algorithms for Calculating Microarray Enrichment (ACME). ACME (Algorithms for Calculating Microar...7 versions - Latest release: about 2 years ago - 1 maintainer
Top 7.1% on spack.io
7 versions - Latest release: about 2 years ago - 3 dependent packages - 1 maintainer
r-a4preproc 1.42.0
Automated Affymetrix Array Analysis Preprocessing Package. Utility functions to pre-process data ...7 versions - Latest release: about 2 years ago - 3 dependent packages - 1 maintainer