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 0.7% dependent packages on spack.io
Top 0.7% dependent packages on spack.io
spack.io : r-biobase
Biobase: Base functions for Bioconductor. Functions that are needed by many other packages or which replace R functions.
Registry
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Source
- JSON
purl: pkg:spack/r-biobase
License: Other
Latest release: about 2 years ago
First release: about 2 years ago
Dependent packages: 77
Last synced: 2 days ago
Top 9.5% on spack.io
4 versions - Latest release: almost 2 years ago - 2 dependent packages - 1 maintainer
r-nmf 0.24.0
Algorithms and Framework for Nonnegative Matrix Factorization (NMF). Provides a framework to perf...4 versions - Latest release: almost 2 years ago - 2 dependent packages - 1 maintainer
Top 7.1% on spack.io
5 versions - Latest release: about 2 years ago - 3 dependent packages
trinity 2.6.6
Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a no...5 versions - Latest release: about 2 years ago - 3 dependent packages
r-yarn 1.20.0
Robust Multi-Condition RNA-Seq Preprocessing and Normalization. Expedite large RNA-Seq analyses u...7 versions - Latest release: about 2 years ago - 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
r-watermelon 2.0.0
Illumina 450 methylation array normalization and metrics. 15 flavours of betas and three performa...3 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
r-vsn 3.62.0
Variance stabilization and calibration for microarray data. The package implements a method for n...7 versions - Latest release: about 2 years ago - 1 dependent package - 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-tmixclust 1.16.0
Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Spline...6 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-spem 1.34.0
S-system parameter estimation method. This package can optimize the parameter in S-system models ...7 versions - Latest release: about 2 years ago - 1 dependent package - 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-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-siggenes 1.68.0
Multiple Testing using SAM and Efron's Empirical Bayes Approaches. Identification of differential...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-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-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-rots 1.22.0
Reproducibility-Optimized Test Statistic. Calculates the Reproducibility-Optimized Test Statistic...7 versions - Latest release: about 2 years ago - 1 dependent package - 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-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-quantro 1.28.0
A test for when to use quantile normalization. A data-driven test for the assumptions of quantile...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
r-mergemaid 2.56.0
Merge Maid. The functions in this R extension are intended for cross- study comparison of gene ex...5 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
r-makecdfenv 1.70.0
CDF Environment Maker. This package has two functions. One reads a Affymetrix chip description fi...7 versions - Latest release: about 2 years ago - 1 dependent package - 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
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 9.5% on spack.io
7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-gostats 2.60.0
Tools for manipulating GO and microarrays. A set of tools for interacting with GO and microarray ...7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-globaltest 5.48.0
Testing Groups of Covariates/Features for Association with a Response Variable, with Applications...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-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
r-geoquery 2.62.2
Get data from NCBI Gene Expression Omnibus (GEO). The NCBI Gene Expression Omnibus (GEO) is a pub...7 versions - Latest release: about 2 years ago - 1 dependent package - 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 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
r-genemeta 1.66.0
MetaAnalysis for High Throughput Experiments. A collection of meta- analysis tools for analysing ...7 versions - Latest release: about 2 years ago - 1 dependent package - 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
Top 5.8% on spack.io
7 versions - Latest release: about 2 years ago - 4 dependent packages - 1 maintainer
r-gcrma 2.66.0
Background Adjustment Using Sequence Information. Background adjustment using sequence information.7 versions - Latest release: about 2 years ago - 4 dependent packages - 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-dss 2.42.0
Dispersion shrinkage for sequencing data. DSS is an R library performing differntial analysis for...5 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 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
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
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
Top 9.5% on spack.io
7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-annaffy 1.66.0
Annotation tools for Affymetrix biological metadata. Functions for handling data from Bioconducto...7 versions - Latest release: about 2 years ago - 2 dependent packages - 1 maintainer
r-analysispageserver 1.18.1
A framework for sharing interactive data and plots from R through the web. AnalysisPageServer is ...5 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-aims 1.26.0
Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype. This package contains the AIMS ...7 versions - Latest release: about 2 years ago - 1 maintainer
r-agimicrorna 2.44.0
Processing and Differential Expression Analysis of Agilent microRNA chips. Processing and Analysi...7 versions - Latest release: about 2 years ago - 1 maintainer
r-agdex 1.42.0
Agreement of Differential Expression Analysis. A tool to evaluate agreement of differential expre...7 versions - Latest release: about 2 years ago - 1 maintainer
r-affyqcreport 1.68.0
QC Report Generation for affyBatch objects. This package creates a QC report for an AffyBatch obj...6 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-affyilm 1.46.0
Linear Model of background subtraction and the Langmuir isotherm. affyILM is a preprocessing tool...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
r-affycontam 1.52.0
structured corruption of affymetrix cel file data. structured corruption of cel file data to demo...7 versions - Latest release: about 2 years ago - 1 maintainer
r-affycomp 1.70.0
Graphics Toolbox for Assessment of Affymetrix Expression Measures. The package contains functions...7 versions - Latest release: about 2 years ago - 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-adsplit 1.64.0
Annotation-Driven Clustering. This package implements clustering of microarray gene expression pr...7 versions - Latest release: about 2 years ago - 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
r-acgh 1.72.0
Classes and functions for Array Comparative Genomic Hybridization data. Functions for reading aCG...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
Top 7.1% on spack.io
7 versions - Latest release: about 2 years ago - 3 dependent packages - 1 maintainer
r-a4core 1.42.0
Automated Affymetrix Array Analysis Core Package. Utility functions for the Automated Affymetrix ...7 versions - Latest release: about 2 years ago - 3 dependent packages - 1 maintainer
r-a4classif 1.42.0
Automated Affymetrix Array Analysis Classification Package. Functionalities for classification of...7 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
r-a4base 1.42.0
Automated Affymetrix Array Analysis Base Package. Base utility functions are available for the Au...7 versions - Latest release: about 2 years ago - 1 dependent package - 1 maintainer