k3ylabs/cosoco-image-dataset huggingface dataset:
Package: r-bioc-destiny (3.8.1-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/destiny/
Depends: r-base-core (>= 4.1.2-1ubuntu2), r-api-4.0, r-api-bioc-3.14, r-cran-matrix, r-cran-rcpp (>= 0.10.3), r-cran-rcppeigen, r-cran-rspectra (>= 0.14-0), r-cran-irlba, r-bioc-pcamethods, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-summarizedexperiment, r-bioc-singlecellexperiment, r-cran-ggplot2, r-cran-ggplot.multistats, r-cran-tidyr, r-cran-tidyselect, r-cran-ggthemes, r-cran-vim, r-cran-knn.covertree, r-cran-proxy, r-cran-rcpphnsw, r-cran-smoother, r-cran-scales, r-cran-scatterplot3d, libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2)
Description:  GNU R diffusion maps This BioConductor package creates and plots diffusion maps.
Package: r-bioc-dexseq (1.40.0+dfsg-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/DEXSeq/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-biocparallel, r-bioc-biobase, r-bioc-summarizedexperiment, r-bioc-iranges (>= 2.5.17), r-bioc-genomicranges (>= 1.23.7), r-bioc-deseq2 (>= 1.9.11), r-bioc-annotationdbi, r-cran-rcolorbrewer, r-bioc-s4vectors (>= 0.23.18), r-bioc-biocgenerics, r-bioc-biomart, r-cran-hwriter, r-cran-stringr, r-bioc-rsamtools, r-cran-statmod, r-bioc-geneplotter, r-bioc-genefilter
Description:  GNU R inference of differential exon usage in RNA-Seq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.
Package: r-bioc-dir.expiry (1.2.0+ds-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/dir.expiry/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-cran-filelock
Description:  Bioconductor managing expiration for cache directories Implements an expiration system for access to versioned directories. Directories that have not been accessed by a registered function within a certain time frame are deleted. This aims to reduce disk usage by eliminating obsolete caches generated by old versions of packages.
Package: r-bioc-dirichletmultinomial (1.36.0-1build1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/DirichletMultinomial/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-s4vectors, r-bioc-iranges, r-bioc-biocgenerics, libc6 (>= 2.29), libgsl27 (>= 2.7.1)
Description:  Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE.
Package: r-bioc-dnacopy (1.68.0-1)
Section: universe/gnu-r
Homepage: https://www.bioconductor.org/packages/DNAcopy/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, libc6 (>= 2.29), libgfortran5 (>= 10)
Description:  R package: DNA copy number data analysis Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number. . This package is for analyzing array DNA copy number data, which is usually (but not always) called array Comparative Genomic Hybridization (array CGH) data It implements a methodology for finding change-points in these data which are points after which the (log) test over reference ratios have changed location. This model is that the change-points correspond to positions where the underlying DNA copy number has changed. Therefore, change-points can be used to identify regions of gained and lost copy number. Also provided is a function for making relevant plots of these data.
Package: r-bioc-drimseq (1.22.0-2)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/DRIMSeq/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-cran-mass, r-bioc-genomicranges, r-bioc-iranges, r-bioc-s4vectors, r-bioc-biocgenerics, r-bioc-biocparallel, r-bioc-limma, r-bioc-edger, r-cran-ggplot2, r-cran-reshape2
Description:  Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results.
Package: r-bioc-dropletutils (1.14.2+ds-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/DropletUtils/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-singlecellexperiment, r-cran-matrix, r-cran-rcpp, r-bioc-biocgenerics, r-bioc-s4vectors, r-bioc-iranges, r-bioc-genomicranges, r-bioc-summarizedexperiment, r-bioc-biocparallel, r-bioc-delayedarray, r-bioc-delayedmatrixstats, r-bioc-hdf5array, r-bioc-rhdf5, r-bioc-edger, r-cran-r.utils, r-cran-dqrng, r-bioc-beachmat, r-bioc-scuttle, r-bioc-rhdf5lib, r-cran-bh, libc6 (>= 2.29), libgcc-s1 (>= 3.0), libhdf5-103-1, libhdf5-cpp-103-1 (>= 1.10.5), libstdc++6 (>= 11)
Description:  BioConductor utilities for handling single-cell droplet data Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading from count matrices or molecule information files, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.
Package: r-bioc-dupradar (1.24.0+ds-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/dupRadar/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-rsubread (>= 1.14.1)
Description:  BioConductor assessment of duplication rates in RNA-Seq datasets This BioConductor package provides assessment of duplication rate quality control for RNA-Seq datasets.
Package: r-bioc-ebseq (1.34.0-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/EBSeq/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-cran-blockmodeling, r-cran-gplots, r-cran-testthat
Description:  R package for RNA-Seq Differential Expression Analysis r-bioc-ebseq is an R package for identifying genes and isoforms differentially expressed (DE) across two or more biological conditions in an RNA-seq experiment.
Package: r-bioc-edaseq (2.28.0+dfsg-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/EDASeq/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-biobase (>= 2.15.1), r-bioc-shortread (>= 1.11.42), r-bioc-biocgenerics, r-bioc-iranges (>= 1.13.9), r-bioc-aroma.light, r-bioc-rsamtools (>= 1.5.75), r-bioc-biomart, r-bioc-biostrings, r-bioc-annotationdbi, r-bioc-genomicfeatures, r-bioc-genomicranges, r-cran-biocmanager
Description:  GNU R exploratory data analysis and normalization for RNA-Seq Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).
Package: r-bioc-edger (3.36.0+dfsg-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/edgeR/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-limma (>= 3.41.5), r-cran-locfit, r-cran-rcpp, libblas3 | libblas.so.3, libc6 (>= 2.29), libgcc-s1 (>= 3.0), liblapack3 | liblapack.so.3, libstdc++6 (>= 5.2)
Description:  Empirical analysis of digital gene expression data in R Bioconductor package for differential expression analysis of whole transcriptome sequencing (RNA-seq) and digital gene expression profiles with biological replication. It uses empirical Bayes estimation and exact tests based on the negative binomial distribution. It is also useful for differential signal analysis with other types of genome-scale count data.
Package: r-bioc-eir (1.34.0+ds-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/eiR/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-chemminer (>= 2.15.15), r-cran-dbi, r-cran-snow, r-cran-snowfall, r-cran-runit, r-cran-rcurl, r-cran-digest, r-bioc-biocgenerics, r-cran-rcppannoy (>= 0.0.9), libc6 (>= 2.2.5)
Description:  Accelerated similarity searching of small molecules The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.
Package: r-bioc-ensembldb (2.18.3+dfsg-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/ensembldb/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-biocgenerics (>= 0.15.10), r-bioc-genomicranges (>= 1.31.18), r-bioc-genomicfeatures (>= 1.29.10), r-bioc-annotationfilter (>= 1.5.2), r-cran-rsqlite (>= 1.1), r-cran-dbi, r-bioc-biobase, r-bioc-genomeinfodb, r-bioc-annotationdbi (>= 1.31.19), r-bioc-rtracklayer, r-bioc-s4vectors (>= 0.23.10), r-bioc-rsamtools, r-bioc-iranges (>= 2.13.24), r-bioc-protgenerics, r-bioc-biostrings (>= 2.47.9), r-cran-curl
Description:  GNU R utilities to create and use an Ensembl based annotation database The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, the ensembldb package provides also a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes.
Package: r-bioc-experimenthub (2.2.1+ds-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/ExperimentHub/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-biocgenerics (>= 0.15.10), r-bioc-annotationhub (>= 2.19.3), r-bioc-biocfilecache (>= 1.5.1), r-bioc-s4vectors, r-cran-biocmanager, r-cran-curl, r-cran-rappdirs
Description:  BioConductor client to access ExperimentHub resources This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.
Package: r-bioc-fishpond (2.0.1+ds-2)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/fishpond/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-cran-abind, r-cran-gtools, r-bioc-qvalue, r-bioc-s4vectors, r-bioc-summarizedexperiment, r-cran-matrixstats, r-cran-svmisc, r-cran-rcpp, r-cran-matrix, r-bioc-singlecellexperiment, r-cran-jsonlite, libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2)
Description:  Differential transcript and gene expression with inferential replicates Fishpond contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling. Also the package contains utilities for working with Salmon and Alevin quantification files.
Package: r-bioc-fmcsr (1.36.0+dfsg-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/fmcsR/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-chemminer, r-cran-runit, r-bioc-biocgenerics, libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 11)
Description:  GNU R mismatch tolerant maximum common substructure searching The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.
Package: r-bioc-genefilter (1.76.0-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/genefilter/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-biocgenerics, r-bioc-annotationdbi, r-bioc-annotate, r-bioc-biobase, r-cran-survival, libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 5)
Description:  methods for filtering genes from microarray experiments This BioConductor module provides methods for filtering genes from microarray experiments.  It contains some basic functions for filtering genes.
Package: r-bioc-genelendatabase (1.30.0-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/data/experiment/geneLenDataBase/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-rtracklayer, r-bioc-genomicfeatures (>= 1.3.15)
Description:  GNU R lengths of mRNA transcripts for a number of genomes This GNU R package calculates length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser.
Package: r-bioc-geneplotter (1.72.0-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/geneplotter/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-biobase, r-bioc-biocgenerics, r-cran-lattice, r-bioc-annotate, r-bioc-annotationdbi, r-cran-rcolorbrewer
Description:  R package of functions for plotting genomic data Geneplotter contains plotting functions for microarrays. . The functions cPlot and cColor allow the user to associate microarray expression data with chromosomal location. The plots can include any subset (by default all chromosomes are shown) of chromosomes for the organism being considered.
Package: r-bioc-genomeinfodb (1.30.1-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/GenomeInfoDb/
Depends: r-base-core (>= 4.1.2-1ubuntu2), r-api-4.0, r-api-bioc-3.14, r-bioc-biocgenerics (>= 0.37.0), r-bioc-s4vectors (>= 0.25.12), r-bioc-iranges (>= 2.13.12), r-cran-rcurl, r-bioc-genomeinfodbdata
Description:  BioConductor utilities for manipulating chromosome identifiers This package contains BioConductor utilities for manipulating chromosome and other 'seqname' identifiers. . The Seqnames package contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.
Package: r-bioc-genomeinfodbdata (1.2.7-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/GenomeInfoDbData/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0
Description:  BioConductor species and taxonomy ID look up tables This package contains files for mapping between NCBI taxonomy ID and species. . It is used by functions in the r-bioc-genomeinfodb package.
Package: r-bioc-genomicalignments (1.30.0-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/GenomicAlignments/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-biocgenerics (>= 0.37.0), r-bioc-s4vectors (>= 0.27.12), r-bioc-iranges (>= 2.23.9), r-bioc-genomeinfodb (>= 1.13.1), r-bioc-genomicranges (>= 1.41.5), r-bioc-summarizedexperiment (>= 1.9.13), r-bioc-biostrings (>= 2.55.7), r-bioc-rsamtools (>= 1.31.2), r-bioc-biocparallel, libc6 (>= 2.4)
Description:  BioConductor representation and manipulation of short genomic alignments This BioConductor package provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.
Package: r-bioc-genomicfeatures (1.46.4+dfsg-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/GenomicFeatures/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-biocgenerics (>= 0.1.0), r-bioc-s4vectors (>= 0.17.29), r-bioc-iranges (>= 2.13.23), r-bioc-genomeinfodb (>= 1.25.7), r-bioc-genomicranges (>= 1.31.17), r-bioc-annotationdbi (>= 1.41.4), r-cran-dbi, r-cran-rsqlite (>= 2.0), r-cran-rcurl, r-bioc-xvector (>= 0.19.7), r-bioc-biostrings (>= 2.47.6), r-bioc-biocio, r-bioc-rtracklayer (>= 1.51.5), r-bioc-biomart (>= 2.17.1), r-bioc-biobase (>= 2.15.1)
Description:  GNU R tools for making and manipulating transcript centric annotations A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.
Package: r-bioc-genomicfiles (1.30.0-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/GenomicFiles/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-biocgenerics (>= 0.11.2), r-bioc-matrixgenerics, r-bioc-genomicranges (>= 1.31.16), r-bioc-summarizedexperiment, r-bioc-biocparallel (>= 1.1.0), r-bioc-rsamtools (>= 1.17.29), r-bioc-rtracklayer (>= 1.25.3), r-bioc-genomicalignments (>= 1.7.7), r-bioc-iranges, r-bioc-s4vectors (>= 0.9.25), r-bioc-variantannotation (>= 1.27.9), r-bioc-genomeinfodb
Description:  Distributed computing by file or by range This package provides infrastructure for parallel computations distributed 'by file' or 'by range'. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation.
Package: r-bioc-genomicranges (1.46.1+dfsg-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/GenomicRanges/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-biocgenerics (>= 0.37.0), r-bioc-s4vectors (>= 0.27.12), r-bioc-iranges (>= 2.23.9), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-xvector (>= 0.29.2), libc6 (>= 2.4)
Description:  BioConductor representation and manipulation of genomic intervals The ability to efficiently store genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing data (a.k.a. NGS data). The package defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.
Package: r-bioc-geoquery (2.62.2+dfsg-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/GEOquery/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-biobase, r-cran-httr, r-cran-readr (>= 1.3.1), r-cran-xml2, r-cran-dplyr, r-cran-data.table, r-cran-tidyr, r-cran-magrittr, r-cran-r.utils, r-bioc-limma
Description:  Get data from NCBI Gene Expression Omnibus (GEO) The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.
Package: r-bioc-ggbio (1.42.0-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/ggbio/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-biocgenerics, r-cran-ggplot2 (>= 1.0.0), r-cran-gridextra, r-cran-scales, r-cran-reshape2, r-cran-gtable, r-cran-hmisc, r-bioc-biovizbase (>= 1.29.2), r-bioc-biobase, r-bioc-s4vectors (>= 0.13.13), r-bioc-iranges (>= 2.11.16), r-bioc-genomeinfodb (>= 1.1.3), r-bioc-genomicranges (>= 1.29.14), r-bioc-summarizedexperiment, r-bioc-biostrings, r-bioc-rsamtools (>= 1.17.28), r-bioc-genomicalignments (>= 1.1.16), r-bioc-bsgenome, r-bioc-variantannotation (>= 1.11.4), r-bioc-rtracklayer (>= 1.25.16), r-bioc-genomicfeatures (>= 1.29.11), r-bioc-organismdbi, r-cran-ggally, r-bioc-ensembldb (>= 1.99.13), r-bioc-annotationdbi, r-bioc-annotationfilter, r-cran-rlang
Description:  Visualization tools for genomic data The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.
Package: r-bioc-glmgampoi (1.6.0+dfsg-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/glmGamPoi/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-cran-rcpp, r-bioc-delayedmatrixstats, r-cran-matrixstats, r-bioc-delayedarray, r-bioc-hdf5array, r-bioc-summarizedexperiment, r-bioc-biocgenerics, r-cran-rcpparmadillo, r-bioc-beachmat, libblas3 | libblas.so.3, libc6 (>= 2.29), libgcc-s1 (>= 3.0), liblapack3 | liblapack.so.3, libstdc++6 (>= 11)
Description:  GNU R fit a Gamma-Poisson generalized linear model Fit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments.
Package: r-bioc-go.db (3.14.0-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/GO.db/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-bioc-annotationdbi (>= 1.55.1)
Description:  annotation maps describing the entire Gene Ontology This package is part of BioConductor and provides a set of annotation maps describing the entire Gene Ontology assembled using data from GO. . The package helps running the test suites of some BioConductor packages.
Package: r-bioc-gosemsim (2.20.0-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/GOSemSim/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-bioc-annotationdbi, r-bioc-go.db, r-cran-rcpp, libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2)
Description:  GO-terms semantic similarity measures The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.
Package: r-bioc-goseq (1.46.0-1)
Section: universe/gnu-r
Homepage: https://bioconductor.org/packages/goseq/
Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14, r-cran-biasedurn, r-bioc-genelendatabase (>= 1.9.2), r-cran-mgcv, r-bioc-annotationdbi, r-bioc-go.db, r-bioc-biocgenerics
Description:  GNU R gene ontology analyser for RNA-seq and other length biased data This GNU R package provides functions to detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.