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Enter the query into the form above. You can look for specific version of a package by using @ symbol like this: gcc@10.

API method:

GET /api/packages?search=hello&page=1&limit=20

where search is your query, page is a page number and limit is a number of items on a single page. Pagination information (such as a number of pages and etc) is returned in response headers.

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r-hdo-db 1.0.0
Propagated dependencies: r-annotationdbi@1.72.0 r-dbi@1.2.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/HDO.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation maps describing the entire Human Disease Ontology
Description:

This package provides a set of annotation maps describing the entire Human Disease Ontology. The annotation data comes from https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology.

r-scds 1.26.0
Propagated dependencies: r-dplyr@1.1.4 r-matrix@1.7-4 r-proc@1.19.0.1 r-s4vectors@0.48.0 r-singlecellexperiment@1.32.0 r-summarizedexperiment@1.40.0 r-xgboost@1.7.11.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/scds
Licenses: Expat
Build system: r
Synopsis: In-silico doublet annotation for single cell RNA sequencing data
Description:

This is an R package for doublet annotation of single cell RNA sequencing data. scds provides methods to annotate doublets in scRNA-seq data computationally.

r-rhisat2 1.26.0
Propagated dependencies: r-genomicranges@1.62.0 r-sgseq@1.44.0 r-txdbmaker@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/fmicompbio/Rhisat2
Licenses: GPL 3
Build system: r
Synopsis: R Wrapper for HISAT2 sequence aligner
Description:

This package provides an R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.

r-rhdf5 2.54.0
Propagated dependencies: r-rhdf5filters@1.22.0 r-rhdf5lib@1.32.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/rhdf5
Licenses: Artistic License 2.0
Build system: r
Synopsis: HDF5 interface to R
Description:

This R/Bioconductor package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

r-pwalign 1.6.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-iranges@2.44.0 r-s4vectors@0.48.0 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/pwalign
Licenses: Artistic License 2.0
Build system: r
Synopsis: Perform pairwise sequence alignments
Description:

The two main functions in the package are pairwiseAlignment and stringDist. The former solves (Needleman-Wunsch) global alignment, (Smith-Waterman) local alignment, and (ends-free) overlap alignment problems. The latter computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.

r-bags 2.50.0
Propagated dependencies: r-biobase@2.70.0 r-breastcancervdx@1.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BAGS
Licenses: Artistic License 2.0
Build system: r
Synopsis: Bayesian approach for geneset selection
Description:

This R package is providing functions to perform geneset significance analysis over simple cross-sectional data between 2 and 5 phenotypes of interest.

r-airway 1.30.0
Propagated dependencies: r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/airway
Licenses: LGPL 2.0+
Build system: r
Synopsis: RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells
Description:

This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells. PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778.

r-affycompatible 1.58.0
Propagated dependencies: r-biostrings@2.78.0 r-rcurl@1.98-1.17 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AffyCompatible/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Work with Affymetrix GeneChip files
Description:

This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. It also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.

r-hypergraph 1.82.0
Propagated dependencies: r-graph@1.88.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/hypergraph
Licenses: Artistic License 2.0
Build system: r
Synopsis: Hypergraph data structures
Description:

This package implements some simple capabilities for representing and manipulating hypergraphs.

r-roc 1.86.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/ROC/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Utilities for ROC curves
Description:

This package provides utilities for Receiver Operating Characteristic (ROC) curves, with a focus on micro arrays.

r-motifstack 1.54.0
Propagated dependencies: r-ade4@1.7-23 r-biostrings@2.78.0 r-ggplot2@4.0.1 r-htmlwidgets@1.6.4 r-tfbstools@1.48.0 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/motifStack/
Licenses: GPL 2+
Build system: r
Synopsis: Plot stacked logos for DNA, RNA and amino acid sequences
Description:

The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motifs and amino acid sequence motifs. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.

r-anvil 1.22.0
Propagated dependencies: r-anvilbase@1.4.0 r-biocbaseutils@1.12.0 r-dplyr@1.1.4 r-dt@0.34.0 r-futile-logger@1.4.3 r-gcptools@1.0.0 r-htmltools@0.5.8.1 r-httr@1.4.7 r-jsonlite@2.0.0 r-miniui@0.1.2 r-rapiclient@0.1.8 r-shiny@1.11.1 r-tibble@3.3.0 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AnVIL
Licenses: Artistic License 2.0
Build system: r
Synopsis: Provides access to AnVIL, Terra, Leonardo and other projects
Description:

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVIL package provides end-user and developer functionality. AnVIL provides fast binary package installation, utilities for working with Terra/AnVIL table and data resources, and convenient functions for file movement to and from Google cloud storage. For developers, AnVIL provides programmatic access to the Terra, Leonardo, Rawls, Dockstore, and Gen3 RESTful programming interface, including helper functions to transform JSON responses to formats more amenable to manipulation in R.

r-bsgenome-drerio-ucsc-danrer10 1.4.2
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer10
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Danio rerio (UCSC version danRer10)
Description:

This package provides full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer10, Sep. 2014) and stored in Biostrings objects.

r-graph 1.88.0
Propagated dependencies: r-biocgenerics@0.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/graph
Licenses: Artistic License 2.0
Build system: r
Synopsis: Handle graph data structures in R
Description:

This package implements some simple graph handling capabilities for R.

r-biobroom 1.42.0
Propagated dependencies: r-biobase@2.70.0 r-broom@1.0.10 r-dplyr@1.1.4 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/StoreyLab/biobroom
Licenses: LGPL 3+
Build system: r
Synopsis: Turn Bioconductor objects into tidy data frames
Description:

This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.

r-toast 1.24.0
Propagated dependencies: r-corpcor@1.6.10 r-doparallel@1.0.17 r-epidish@2.26.0 r-ggally@2.4.0 r-ggplot2@4.0.1 r-limma@3.66.0 r-nnls@1.6 r-quadprog@1.5-8 r-summarizedexperiment@1.40.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/TOAST
Licenses: GPL 2
Build system: r
Synopsis: Tools for the analysis of heterogeneous tissues
Description:

This package is devoted to analyzing high-throughput data (e.g. gene expression microarray, DNA methylation microarray, RNA-seq) from complex tissues. Current functionalities include

  1. detect cell-type specific or cross-cell type differential signals

  2. tree-based differential analysis

  3. improve variable selection in reference-free deconvolution

  4. partial reference-free deconvolution with prior knowledge.

r-annotationtools 1.84.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/annotationTools/
Licenses: GPL 2+
Build system: r
Synopsis: Annotate microarrays and perform gene expression analyses
Description:

This package provides functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files).

r-bsgenome-mmusculus-ucsc-mm9-masked 1.3.99
Propagated dependencies: r-bsgenome@1.78.0 r-bsgenome-mmusculus-ucsc-mm9@1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full masked genome sequences for Mouse
Description:

This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

r-mdqc 1.72.0
Propagated dependencies: r-cluster@2.1.8.1 r-mass@7.3-65
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/mdqc
Licenses: LGPL 2.0+
Build system: r
Synopsis: Mahalanobis distance quality control for microarrays
Description:

MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.

r-chicago 1.38.0
Propagated dependencies: r-data-table@1.17.8 r-delaporte@8.4.2 r-hmisc@5.2-4 r-mass@7.3-65 r-matrixstats@1.5.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Chicago
Licenses: Artistic License 2.0
Build system: r
Synopsis: Capture Hi-C analysis of genomic organization
Description:

This package provides a pipeline for analysing Capture Hi-C data.

r-alabaster-matrix 1.10.0
Propagated dependencies: r-alabaster-base@1.10.0 r-biocgenerics@0.56.0 r-delayedarray@0.36.0 r-hdf5array@1.38.0 r-matrix@1.7-4 r-rcpp@1.1.0 r-rhdf5@2.54.0 r-s4arrays@1.10.0 r-s4vectors@0.48.0 r-sparsearray@1.10.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/alabaster.matrix
Licenses: Expat
Build system: r
Synopsis: Load and save artifacts from file
Description:

This is a package for saving matrices, arrays and similar objects into file artifacts, and loading them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

r-sictools 1.40.0
Dependencies: ncurses@6.2.20210619
Propagated dependencies: r-biostrings@2.78.0 r-doparallel@1.0.17 r-genomicranges@1.62.0 r-iranges@2.44.0 r-matrixstats@1.5.0 r-plyr@1.8.9 r-rsamtools@2.26.0 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/SICtools
Licenses: GPL 2+
Build system: r
Synopsis: Find SNV/Indel differences between two bam files with near relationship
Description:

This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison through each base position across the genome region of interest. The difference is inferred by Fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.

r-txdbmaker 1.6.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocio@1.20.0 r-biomart@2.66.0 r-dbi@1.2.3 r-genomeinfodb@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-httr@1.4.7 r-iranges@2.44.0 r-rjson@0.2.23 r-rsqlite@2.4.4 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-ucsc-utils@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/txdbmaker
Licenses: Artistic License 2.0
Build system: r
Synopsis: Tools for making TxDb objects from genomic annotations
Description:

This package provides a set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.

r-rnaseqdata-hnrnpc-bam-chr14 0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1147/
Licenses: LGPL 2.0+
Build system: r
Synopsis: Aligned reads from RNAseq experiment
Description:

The package contains 8 BAM files, 1 per sequencing run. Each BAM file was obtained by aligning the reads (paired-end) to the full hg19 genome with TopHat2, and then subsetting to keep only alignments on chr14. See accession number E-MTAB-1147 in the ArrayExpress database for details about the experiment, including links to the published study (by Zarnack et al., 2012) and to the FASTQ files.

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Total results: 68655