Software Packages in "experimental", Subsection gnu-r

python3-mofapy (1.6.1 dfsg-14)
Multi-Omics Factor Analysis (MOFA) - Python module
r-bioc-affxparser (1.78.0-1)
Affymetrix File Parsing SDK
r-bioc-affy (1.84.0-1)
BioConductor methods for Affymetrix Oligonucleotide Arrays
r-bioc-affyio (1.76.0-1)
BioConductor tools for parsing Affymetrix data files
r-bioc-alabaster.base (1.6.1 ds-1 b1)
Save Bioconductor Objects To File
r-bioc-alabaster.matrix (1.6.1 ds-1)
Load and Save matrices, arrays, and similar objects from files
r-bioc-alabaster.ranges (1.6.0 ds-1)
Load and Save Ranges-related Artifacts from File
r-bioc-alabaster.sce (1.6.0 ds-1)
Load and Save SingleCellExperiment from File
r-bioc-alabaster.schemas (1.6.0 ds-1)
Schemas for the Alabaster Framework
r-bioc-alabaster.se (1.6.0 ds-1)
Load and Save SummarizedExperiments from File
r-bioc-all (1.48.0-1)
Bioconductor data package used by several bioc tools
r-bioc-altcdfenvs (1:2.68.0-1)
BioConductor alternative CDF environments
r-bioc-annotate (1.84.0 dfsg-1)
BioConductor annotation for microarrays
r-bioc-annotationdbi (1.68.0-1)
GNU R Annotation Database Interface for BioConductor
r-bioc-annotationfilter (1.30.0 dfsg-1)
facilities for filtering Bioconductor annotation resources
r-bioc-annotationhub (3.14.0 dfsg-1)
GNU R client to access AnnotationHub resources
r-bioc-aroma.light (3.36.0-1)
BioConductor methods normalization and visualization of microarray data
r-bioc-arrayexpress (1.66.0-1)
access to the ArrayExpress Microarray Database at EBI
r-bioc-ballgown (2.38.0 dfsg-1)
Flexible, isoform-level differential expression analysis
r-bioc-basilisk (1.18.0 ds-1 [amd64, arm64], 1.16.0 ds-2~0exp0 [alpha, mips64el, ppc64, ppc64el, riscv64, s390x, sparc64])
freezing Python dependencies inside Bioconductor packages
r-bioc-basilisk.utils (1.18.0 ds-1)
Bioconductor basilisk installation utilities
r-bioc-biobase (2.66.0-1)
base functions for Bioconductor
r-bioc-biocbaseutils (1.8.0 dfsg-1)
General utility functions for developing Bioconductor packages
r-bioc-bioccheck (1.42.0 dfsg-1)
Bioconductor-specific package checks
r-bioc-biocfilecache (2.14.0 dfsg-1)
GNU R management of files across sessions
r-bioc-biocgenerics (0.52.0-1)
generic functions for Bioconductor
r-bioc-biocio (1.16.0 dfsg-1)
standard input and output for Bioconductor packages
r-bioc-biocparallel (1.40.0-1)
BioConductor facilities for parallel evaluation
r-bioc-biocversion (3.20.0-1~0exp0)
set the appropriate version of Bioconductor packages
r-bioc-biocviews (1.74.0-1)
Categorized views of R package repositories
r-bioc-biomart (2.62.0 dfsg-1)
GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)
r-bioc-biomformat (1.34.0 dfsg-1)
GNU R interface package for the BIOM file format
r-bioc-biostrings (2.74.0 dfsg-1)
GNU R string objects representing biological sequences
r-bioc-biovizbase (1.54.0-1)
GNU R basic graphic utilities for visualization of genomic data
r-bioc-bladderbatch (1.44.0-1)
GNU R bladder gene expression data illustrating batch effects
r-bioc-bsgenome (1.74.0-1)
BioConductor infrastructure for Biostrings-based genome data packages
r-bioc-bsseq (1.42.0 dfsg-1)
Bioconductor analyze, manage and store bisulfite sequencing data
r-bioc-chemminer (3.58.0 dfsg-1)
Cheminformatics Toolkit for R
r-bioc-cner (1.42.0 dfsg-1)
CNE Detection and Visualization
r-bioc-complexheatmap (2.22.0 dfsg-1)
make complex heatmaps using GNU R
r-bioc-consensusclusterplus (1.70.0-1)
GNU R determining cluster count and membership
r-bioc-ctc (1.80.0-1)
Cluster and Tree Conversion
r-bioc-cummerbund (2.48.0-1)
tool for analysis of Cufflinks RNA-Seq output
r-bioc-dada2 (1.34.0 dfsg-1)
sample inference from amplicon sequencing data
r-bioc-decontam (1.26.0 dfsg-1)
identify contaminants in marker-gene and metagenomics sequencing sata
r-bioc-decoupler (2.12.0 dfsg-1)
infer biological activities from omics data
r-bioc-degnorm (1.16.0 ds-1)
DegNorm: degradation normalization for RNA-seq data
r-bioc-degreport (1.42.0 dfsg-1)
BioConductor report of DEG analysis
r-bioc-delayedarray (0.32.0 dfsg-1)
BioConductor delayed operations on array-like objects
r-bioc-delayedmatrixstats (1.28.0 ds-1)
Functions on Rows and Columns of 'DelayedMatrix' Objects
r-bioc-demixt (1.22.0-1)
Cell type-specific deconvolution of heterogeneous tumor samples
r-bioc-densvis (1.16.0 dfsg-1 [amd64, arm64, mips64el, ppc64, ppc64el, riscv64, s390x, sparc64], 1.14.0 dfsg-1~0exp1 [alpha])
density-preserving data visualization via non-linear dimensionality reduction
r-bioc-deseq (1.39.0-16)
GNU R differential gene expression analysis
r-bioc-deseq2 (1.46.0 dfsg-1)
R package for RNA-Seq Differential Expression Analysis
r-bioc-destiny (3.20.0-1)
GNU R diffusion maps
r-bioc-dexseq (1.52.0 dfsg-1)
GNU R inference of differential exon usage in RNA-Seq
r-bioc-dir.expiry (1.14.0 ds-1)
Bioconductor managing expiration for cache directories
r-bioc-dirichletmultinomial (1.48.0-1)
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
r-bioc-dnacopy (1.80.0-1)
R package: DNA copy number data analysis
r-bioc-drimseq (1.34.0-1)
Differential transcript usage and tuQTL analyses with
r-bioc-dss (2.54.0 dfsg-1)
Bioconductor dispersion shrinkage for sequencing data
r-bioc-dupradar (1.36.0 ds-1)
BioConductor assessment of duplication rates in RNA-Seq datasets
r-bioc-ebseq (2.4.0-1)
R package for RNA-Seq Differential Expression Analysis
r-bioc-edaseq (2.40.0 dfsg-1)
GNU R exploratory data analysis and normalization for RNA-Seq
r-bioc-edger (4.4.1 dfsg-1)
Empirical analysis of digital gene expression data in R
r-bioc-eir (1.46.0 ds-1)
Accelerated similarity searching of small molecules
r-bioc-ensembldb (2.30.0 dfsg-1)
GNU R utilities to create and use an Ensembl based annotation database
r-bioc-experimenthub (2.14.0 ds-1)
BioConductor client to access ExperimentHub resources
r-bioc-fishpond (2.12.0 ds-1)
Differential transcript and gene expression with inferential replicates
r-bioc-fmcsr (1.48.0 dfsg-1)
GNU R mismatch tolerant maximum common substructure searching
r-bioc-genefilter (1.88.0-1)
methods for filtering genes from microarray experiments
r-bioc-genelendatabase (1.42.0-1)
GNU R lengths of mRNA transcripts for a number of genomes
r-bioc-geneplotter (1.84.0 dfsg-1)
R package of functions for plotting genomic data
r-bioc-genomeinfodb (1.42.1 dfsg-1)
BioConductor utilities for manipulating chromosome identifiers
r-bioc-genomeinfodbdata (1.2.13-1)
BioConductor species and taxonomy ID look up tables
r-bioc-genomicalignments (1.42.0-1)
BioConductor representation and manipulation of short genomic alignments
r-bioc-genomicfeatures (1.58.0 dfsg-1)
GNU R tools for making and manipulating transcript centric annotations
r-bioc-genomicfiles (1.42.0 dfsg-1)
Distributed computing by file or by range
r-bioc-genomicranges (1.58.0 dfsg-1)
BioConductor representation and manipulation of genomic intervals
r-bioc-geoquery (2.74.0 dfsg-1)
Get data from NCBI Gene Expression Omnibus (GEO)
r-bioc-ggbio (1.54.0-1)
Visualization tools for genomic data
r-bioc-go.db (3.20.0-1)
annotation maps describing the entire Gene Ontology
r-bioc-golubesets (1.48.0-1)
exprSets for golub leukemia data
r-bioc-gosemsim (2.32.0-1)
GO-terms semantic similarity measures
r-bioc-goseq (1.58.0-1)
GNU R gene ontology analyser for RNA-seq and other length biased data
r-bioc-graph (1.84.0-1)
handle graph data structures for BioConductor
r-bioc-grohmm (1.38.0-2)
GRO-seq Analysis Pipeline
r-bioc-gseabase (1.68.0 ds-1)
Gene set enrichment data structures and methods
r-bioc-gsva (2.0.2 ds-1)
Gene Set Variation Analysis for microarray and RNA-seq data
r-bioc-gsvadata (1.42.0-1)
Data employed in the vignette of the GSVA package
r-bioc-gviz (1.50.0 dfsg-1)
Plotting data and annotation information along genomic coordinates
r-bioc-gypsum (1.2.0 ds-1)
Interface to the gypsum REST API
r-bioc-hdf5array (1.34.0-1 b1)
HDF5 backend for DelayedArray objects
r-bioc-hsmmsinglecell (1.26.0-1)
Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts
r-bioc-htsfilter (1.46.0 dfsg-1)
GNU R filter replicated high-throughput transcriptome sequencing data
r-bioc-hypergraph (1.78.0-1)
BioConductor hypergraph data structures
r-bioc-ihw (1.34.0 dfsg-1)
GNU R independent hypothesis weighting
r-bioc-impute (1.80.0-1)
Imputation for microarray data
r-bioc-interactivedisplaybase (1.44.0 dfsg-1)
base package for enabling powerful shiny web displays of Bioconductor objects
r-bioc-ioniser (2.30.0 dfsg-1)
Quality Assessment Tools for Oxford Nanopore MinION data
r-bioc-iranges (2.40.0-1)
GNU R low-level containers for storing sets of integer ranges
r-bioc-isoformswitchanalyzer (2.6.0 ds-1)
Identify, Annotate and Visualize Alternative Splicing and
r-bioc-keggrest (1.46.0 dfsg-1)
GNU R client-side REST access to KEGG
r-bioc-limma (3.62.1 dfsg-1)
linear models for microarray data
r-bioc-lpsymphony (1.34.0 dfsg-1)
Symphony integer linear programming solver in GNU R
r-bioc-makecdfenv (1.82.0-1)
BioConductor CDF Environment Maker
r-bioc-matrixgenerics (1.18.0-1)
S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
r-bioc-megadepth (1.16.0 ds-1)
BioCOnductor BigWig and BAM related utilities
r-bioc-mergeomics (1.34.0-1)
Integrative network analysis of omics data
r-bioc-metagenomeseq (1.46.0-2)
GNU R statistical analysis for sparse high-throughput sequencing
r-bioc-metapod (1.14.0 dfsg-1)
GNU R meta-analyses on P-Values of differential analyses
r-bioc-mofa (1.6.1 dfsg-14)
Multi-Omics Factor Analysis (MOFA)
r-bioc-monocle (2.34.0-1)
clustering, differential expression, and trajectory analysis for RNA-Seq
r-bioc-multiassayexperiment (1.32.0 dfsg-1)
Software for integrating multi-omics experiments in BioConductor
r-bioc-multtest (2.62.0-1)
Bioconductor resampling-based multiple hypothesis testing
r-bioc-mutationalpatterns (3.16.0 dfsg-1)
GNU R comprehensive genome-wide analysis of mutational processes
r-bioc-netsam (1.46.0-1)
Network Seriation And Modularization
r-bioc-noiseq (2.50.0-1)
Exploratory analysis and differential expression for RNA-seq data
r-bioc-oligo (1.70.0 ds-1)
Preprocessing tools for oligonucleotide arrays
r-bioc-oligoclasses (1.68.0-1)
Classes for high-throughput arrays supported by oligo and crlmm
r-bioc-org.hs.eg.db (3.20.0-1)
genome-wide annotation for Human
r-bioc-organismdbi (1.48.0 dfsg-1)
smooth interfacing of different database packages
r-bioc-pcamethods (1.98.0-1)
BioConductor collection of PCA methods
r-bioc-pfamanalyzer (1.6.0 dfsg-1)
GNU R identification of domain isotypes in pfam data
r-bioc-phyloseq (1.50.0 dfsg-1)
GNU R handling and analysis of high-throughput microbiome census data
r-bioc-preprocesscore (1.68.0 ds-1)
BioConductor collection of pre-processing functions
r-bioc-progeny (1.28.0 ds-1)
activity inference from gene expression
r-bioc-protgenerics (1.38.0-1)
S4 generic functions for Bioconductor proteomics infrastructure
r-bioc-purecn (2.12.0 dfsg-1)
copy number calling and SNV classification using targeted short read sequencing
r-bioc-pwalign (1.2.0-1)
Perform pairwise sequence alignments
r-bioc-pwmenrich (4.42.0-1)
PWM enrichment analysis
r-bioc-qtlizer (1.20.0 dfsg-1)
Comprehensive QTL annotation of GWAS results
r-bioc-qusage (2.40.0-1)
qusage: Quantitative Set Analysis for Gene Expression
r-bioc-qvalue (2.38.0-1)
GNU R package for Q-value estimation for FDR control
r-bioc-rbgl (1.82.0 dfsg-1)
R interface to the graph algorithms contained in the BOOST library
r-bioc-rcpi (1.42.0 ds-1)
molecular informatics toolkit for compound-protein interaction
r-bioc-rcwl (1.22.0 ds-1)
An R interface to the Common Workflow Language
r-bioc-residualmatrix (1.16.0 dfsg-1)
Creating a DelayedMatrix of Regression Residuals
r-bioc-rgsepd (1.38.0-1)
GNU R gene set enrichment / projection displays
r-bioc-rhdf5 (2.50.0 dfsg-3 b1)
BioConductor HDF5 interface to R
r-bioc-rhdf5filters (1.18.0 dfsg-1)
GNU R HDF5 compression filters
r-bioc-rhdf5lib (1.28.0 dfsg-1 b1)
GNU R hdf5 library
r-bioc-rhtslib (3.2.0 dfsg-1)
HTSlib high-throughput sequencing library as GNU R package
r-bioc-rots (1.34.0-1)
GNU R Teproducibility-Optimized Test Statistic
r-bioc-rsamtools (2.22.0 dfsg-1)
GNU R binary alignment (BAM), variant call (BCF), or tabix file import
r-bioc-rsubread (2.20.0-1)
Subread Sequence Alignment and Counting for R
r-bioc-rtracklayer (1.66.0-1)
GNU R interface to genome browsers and their annotation tracks
r-bioc-rwikipathways (1.26.0 dfsg-1)
GNU R client library for the WikiPathways API
r-bioc-s4arrays (1.6.0 dfsg-1)
foundation of array-like containers in Bioconductor
r-bioc-s4vectors (0.44.0 dfsg-1)
BioConductor S4 implementation of vectors and lists
r-bioc-saturn (1.14.0 dfsg-1)
scalable analysis of differential transcript usage for RNA-sequencing
r-bioc-scaledmatrix (1.14.0 dfsg-1)
creating a DelayedMatrix of scaled and centered values using GNU R
r-bioc-scater (1.34.0 ds-1)
Single-Cell Analysis Toolkit for Gene Expression Data in R
r-bioc-scran (1.34.0 dfsg-1)
BioConductor methods for single-cell RNA-Seq data analysis
r-bioc-scrnaseq (2.20.0 ds-1)
Collection of Public Single-Cell RNA-Seq Datasets
r-bioc-scuttle (1.16.0 dfsg-1)
BioConductor single-cell RNA-Seq analysis utilities
(1.72.0 dfsg-1)
GNU R sequence logos for DNA sequence alignments
r-bioc-shortread (1.64.0-1)
GNU R classes and methods for high-throughput short-read sequencing data
r-bioc-singlecellexperiment (1.28.1 ds-1)
S4 Classes for Single Cell Data
r-bioc-snpstats (1.56.0 dfsg-1)
BioConductor SnpMatrix and XSnpMatrix classes and methods
r-bioc-sparsearray (1.6.0 dfsg-1)
efficient in-memory representation of multidimensional sparse arrays
r-bioc-sparsematrixstats (1.18.0 dfsg-1)
BioConductor summary statistics for rows and columns of sparse matrices
r-bioc-spatialexperiment (1.16.0 ds-1)
S4 Class for Spatially Resolved -omics Data
r-bioc-stringdb (2.18.0-1)
Search Tool for the Retrieval of Interacting proteins database
r-bioc-structuralvariantannotation (1.22.0 ds-1)
Variant annotations for structural variants
r-bioc-summarizedexperiment (1.36.0 dfsg-1)
BioConductor assay container
r-bioc-sva (3.54.0-1)
GNU R Surrogate Variable Analysis
r-bioc-tcgabiolinks (2.34.0 dfsg-1)
GNU R/Bioconductor package for integrative analysis with GDC data
r-bioc-tcgabiolinksgui.data (1.26.0 dfsg-1)
Data for the TCGAbiolinksGUI package
r-bioc-tfbstools (1.44.0 dfsg-1)
GNU R Transcription Factor Binding Site (TFBS) Analysis
r-bioc-titancna (1.44.0-1)
Subclonal copy number and LOH prediction from whole genome sequencing
r-bioc-txdbmaker (1.2.1 ds-1)
Tools for making TxDb objects from genomic annotations
r-bioc-tximeta (1.24.0 dfsg-1)
Transcript Quantification Import with Automatic Metadata
r-bioc-tximport (1.34.0 dfsg-1)
transcript-level estimates for biological sequencing
r-bioc-tximportdata (1.34.0 ds-1)
GNU R various transcript abundance quantifiers
r-bioc-ucsc.utils (1.2.0 ds-1)
Low-level utilities to retrieve data from the UCSC Genome Browser
r-bioc-variantannotation (1.52.0-1)
BioConductor annotation of genetic variants
r-bioc-wrench (1.24.0 dfsg-1)
GNU R wrench normalization for sparse count data
r-bioc-xvector (0.46.0-1)
BioConductor representation and manpulation of external sequences
r-bioc-zlibbioc (1.52.0 dfsg-1)
(Virtual) zlibbioc Bioconductor package
r-cran-ggm (2.5.1-3~0exp0)
GNU R functions for graphical Markov models
r-cran-mutoss (0.1-13-2~0exp0)
GNU R unified multiple testing procedures
r-cran-rmariadb (1.3.2 ds-2~0exp0)
Database Interface and 'MariaDB' Driver