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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.

If you'd like to join our channel webring send a patch to ~whereiseveryone/toys@lists.sr.ht adding your channel as an entry in channels.scm.


r-affycontam 1.68.0
Propagated dependencies: r-affy@1.88.0 r-affydata@1.58.0 r-biobase@2.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/affyContam/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Structured corruption of Affymetrix CEL file data
Description:

Microarray quality assessment is a major concern of microarray analysts. This package provides some simple approaches to in silico creation of quality problems in CEL-level data to help evaluate performance of quality metrics.

r-tcgautils 1.30.1
Propagated dependencies: r-annotationdbi@1.72.0 r-biocbaseutils@1.12.0 r-biocgenerics@0.56.0 r-genomeinfodb@1.46.0 r-genomicdatacommons@1.34.1 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-multiassayexperiment@1.36.1 r-raggedexperiment@1.34.0 r-rvest@1.0.5 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-xml2@1.5.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/TCGAutils
Licenses: Artistic License 2.0
Build system: r
Synopsis: TCGA utility functions for data management
Description:

This package provides a suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.

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-nbpseq 0.3.1
Propagated dependencies: r-qvalue@2.42.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/web/packages/NBPSeq
Licenses: GPL 2
Build system: r
Synopsis: Negative binomial models for RNA-Seq data
Description:

This package provides negative binomial models for two-group comparisons and regression inferences from RNA-sequencing data.

r-mus-musculus 1.3.1
Propagated dependencies: r-annotationdbi@1.72.0 r-genomicfeatures@1.62.0 r-go-db@3.22.0 r-org-mm-eg-db@3.22.0 r-organismdbi@1.52.0 r-txdb-mmusculus-ucsc-mm10-knowngene@3.10.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Mus.musculus
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for the Mus.musculus object
Description:

This package contains the Mus.musculus object to access data from several related annotation packages.

r-org-dr-eg-db 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/org.Dr.eg.db/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation for Zebrafish
Description:

This package provides genome wide annotations for Zebrafish, primarily based on mapping using Entrez Gene identifiers.

r-sesamedata 1.28.0
Propagated dependencies: r-annotationhub@4.0.0 r-experimenthub@3.0.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-readr@2.1.6 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/sesameData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Supporting Data for SeSAMe Package
Description:

This package provides supporting annotation and test data for SeSAMe package. This includes chip tango addresses, mapping information, performance annotation, and trained predictor for Infinium array data. This package provides user access to essential annotation data for working with many generations of the Infinium DNA methylation array. It currently supports human array (HM27, HM450, EPIC), mouse array (MM285) and the HorvathMethylChip40 (Mammal40) array.

r-matrixgenerics 1.22.0
Propagated dependencies: r-matrixstats@1.5.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MatrixGenerics
Licenses: Artistic License 2.0
Build system: r
Synopsis: S4 generic summary statistic functions for matrix-like objects
Description:

This package provides S4 generic functions modeled after the matrixStats API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities.

r-category 2.76.0
Propagated dependencies: r-annotate@1.88.0 r-annotationdbi@1.72.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-dbi@1.2.3 r-genefilter@1.92.0 r-graph@1.88.0 r-gseabase@1.72.0 r-matrix@1.7-4 r-rbgl@1.86.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Category
Licenses: Artistic License 2.0
Build system: r
Synopsis: Category analysis
Description:

This package provides a collection of tools for performing category analysis.

r-cardelino 1.12.0
Propagated dependencies: r-combinat@0.0-8 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-ggtree@4.0.1 r-matrix@1.7-4 r-matrixstats@1.5.0 r-pheatmap@1.0.13 r-s4vectors@0.48.0 r-snpstats@1.60.0 r-variantannotation@1.56.0 r-vcfr@1.15.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/single-cell-genetics/cardelino
Licenses: GPL 3
Build system: r
Synopsis: Clone identification from single cell data
Description:

This package provides methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stochastic dropout events as well as systematic allelic imbalance is used.

r-bambu 3.12.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-bsgenome@1.78.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1 r-rsamtools@2.26.0 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0 r-tidyr@1.3.1 r-xgboost@1.7.11.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/GoekeLab/bambu
Licenses: GPL 3
Build system: r
Synopsis: Isoform reconstruction and quantification for long read RNA-Seq data
Description:

This R package is for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis, such as differential gene expression or transcript usage.

r-beachmat-hdf5 1.8.0
Propagated dependencies: r-assorthead@1.4.0 r-beachmat@2.26.0 r-delayedarray@0.36.0 r-hdf5array@1.38.0 r-rcpp@1.1.0 r-rhdf5lib@1.32.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/beachmat.hdf5
Licenses: GPL 3
Build system: r
Synopsis: beachmat bindings for HDF5-backed matrices
Description:

This package extends beachmat to support initialization of tatami matrices from HDF5-backed arrays. This allows C++ code in downstream packages to directly call the HDF5 C/C++ library to access array data, without the need for block processing via DelayedArray. Some utilities are also provided for direct creation of an in-memory tatami matrix from a HDF5 file.

r-perfmeas 1.2.5
Propagated dependencies: r-graph@1.88.0 r-limma@3.66.0 r-rbgl@1.86.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/web/packages/PerfMeas/
Licenses: GPL 2+
Build system: r
Synopsis: Performance measures for ranking and classification tasks
Description:

This package implements different performance measures for classification and ranking tasks. Area under curve (AUC), precision at a given recall, F-score for single and multiple classes are available.

r-cummerbund 2.50.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-fastcluster@1.3.0 r-ggplot2@4.0.1 r-gviz@1.54.0 r-plyr@1.8.9 r-reshape2@1.4.5 r-rsqlite@2.4.4 r-rtracklayer@1.70.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/cummeRbund/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Analyze Cufflinks high-throughput sequencing data
Description:

This package allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.

r-roar 1.46.0
Propagated dependencies: r-biocgenerics@0.56.0 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/vodkatad/roar/
Licenses: GPL 3
Build system: r
Synopsis: Identify differential APA usage from RNA-seq alignments
Description:

This package provides tools for identifying preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments.

r-txdb-dmelanogaster-ucsc-dm6-ensgene 3.12.0
Propagated dependencies: r-annotationdbi@1.72.0 r-genomicfeatures@1.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for TxDb object(s)
Description:

This package exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

r-somaticsignatures 2.46.0
Propagated dependencies: r-biobase@2.70.0 r-biostrings@2.78.0 r-genomicranges@1.62.0 r-ggbio@1.58.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-nmf@0.28 r-pcamethods@2.2.0 r-proxy@0.4-27 r-reshape2@1.4.5 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/juliangehring/SomaticSignatures
Licenses: Expat
Build system: r
Synopsis: Somatic signatures
Description:

This package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.

r-biosigner 1.38.0
Propagated dependencies: r-biobase@2.70.0 r-e1071@1.7-16 r-multiassayexperiment@1.36.1 r-multidataset@1.38.0 r-randomforest@4.7-1.2 r-ropls@1.42.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/biosigner/
Licenses: CeCILL
Build system: r
Synopsis: Signature discovery from omics data
Description:

Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a method to assess the relevance of the variables for the prediction performances of the classifier. The approach can be run in parallel with the PLS-DA, Random Forest, and SVM binary classifiers. The signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets.

r-motiv 1.43.0
Dependencies: gsl@2.8
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-lattice@0.22-7 r-rgadem@2.55.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MotIV/
Licenses: GPL 2
Build system: r
Synopsis: Motif identification and validation
Description:

This package is used for the identification and validation of sequence motifs. It makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs.

r-genie3 1.32.0
Propagated dependencies: r-dplyr@1.1.4 r-reshape2@1.4.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GENIE3
Licenses: GPL 2+
Build system: r
Synopsis: Gene network inference with ensemble of trees
Description:

This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.

r-cigarillo 1.0.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-iranges@2.44.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/cigarillo
Licenses: Artistic License 2.0
Build system: r
Synopsis: Efficient manipulation of CIGAR strings
Description:

CIGAR stands for Concise Idiosyncratic Gapped Alignment Report. CIGAR strings are found in the BAM files produced by most aligners and in the AIRR-formatted output produced by IgBLAST. The cigarillo package provides functions to parse and inspect CIGAR strings, trim them, turn them into ranges of positions relative to the "query space" or "reference space", and project positions or sequences from one space to the other. Note that these operations are low-level operations that the user rarely needs to perform directly. More typically, they are performed behind the scene by higher-level functionality implemented in other packages like Bioconductor packages GenomicAlignments and igblastr.

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-ripseeker 1.26.0
Propagated dependencies: r-s4vectors@0.48.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-summarizedexperiment@1.40.0 r-rsamtools@2.26.0 r-genomicalignments@1.46.0 r-rtracklayer@1.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/RIPSeeker
Licenses: GPL 2
Build system: r
Synopsis: Identifying protein-associated transcripts from RIP-seq experiments
Description:

This package infers and discriminates RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.

r-gypsum 1.6.0
Propagated dependencies: r-filelock@1.0.3 r-httr2@1.2.1 r-jsonlite@2.0.0 r-rappdirs@0.3.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ArtifactDB/gypsum-R
Licenses: Expat
Build system: r
Synopsis: Interface to the gypsum REST API
Description:

This package provides a client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various administrative and management tasks. Check out the documentation at https://github.com/ArtifactDB/gypsum-worker for more details.

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Total results: 69112