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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-rtcga-clinical 20151101.40.0
Propagated dependencies: r-rtcga@1.38.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RTCGA.clinical
Licenses: GPL 2
Synopsis: Clinical datasets from The Cancer Genome Atlas Project
Description:

Package provides clinical datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Clinical data format is explained here https://wiki.nci.nih.gov/display/TCGA/Clinical+Data+Overview. Data from 2015-11-01 snapshot.

r-rbcbook1 1.78.0
Propagated dependencies: r-rpart@4.1.24 r-graph@1.86.0 r-biobase@2.68.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: http://www.biostat.harvard.edu/~carey
Licenses: Artistic License 2.0
Synopsis: Support for Springer monograph on Bioconductor
Description:

tools for building book.

r-rae230aprobe 2.18.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rae230aprobe
Licenses: LGPL 2.0+
Synopsis: Probe sequence data for microarrays of type rae230a
Description:

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RAE230A\_probe\_tab.

r-rgu34bcdf 2.18.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rgu34bcdf
Licenses: LGPL 2.0+
Synopsis: rgu34bcdf
Description:

This package provides a package containing an environment representing the RG_U34B.cdf file.

r-rbowtiecuda 1.2.0
Dependencies: gcc@14.3.0 cmake@4.0.3
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/FranckRICHARD01/RbowtieCuda
Licenses: Modified BSD
Synopsis: An R Wrapper for nvBowtie and nvBWT, a rewritten version of Bowtie2 for cuda
Description:

This package provides an R wrapper for the popular Bowtie2 sequencing read aligner, optimized to run on NVIDIA graphics cards. It includes wrapper functions that enable both genome indexing and alignment to the generated indexes, ensuring high performance and ease of use within the R environment.

r-rawdiag 1.6.0
Propagated dependencies: r-shiny@1.10.0 r-scales@1.4.0 r-rlang@1.1.6 r-reshape2@1.4.4 r-rawrr@1.18.0 r-htmltools@0.5.8.1 r-hexbin@1.28.5 r-ggplot2@3.5.2 r-dplyr@1.1.4 r-biocparallel@1.42.0 r-biocmanager@1.30.25
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/fgcz/rawDiag/
Licenses: GPL 3
Synopsis: Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful
Description:

Optimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) poses a nontrivial challenge. The rawDiag package facilitates rational method optimization by generating MS operator-tailored diagnostic plots of scan-level metadata. The package is designed for use on the R shell or as a Shiny application on the Orbitrap instrument PC.

r-reactomegsa-data 1.24.0
Propagated dependencies: r-seurat@5.3.0 r-reactomegsa@1.24.0 r-limma@3.64.1 r-edger@4.6.2
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/reactome/ReactomeGSA.data/issues
Licenses: Artistic License 2.0
Synopsis: Companion data package for the ReactomeGSA package
Description:

Companion data sets to showcase the functionality of the ReactomeGSA package. This package contains proteomics and RNA-seq data of the melanoma B-cell induction study by Griss et al. and scRNA-seq data from Jerby-Arnon et al.

r-rebet 1.28.0
Propagated dependencies: r-asset@2.26.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/REBET
Licenses: GPL 2
Synopsis: The subREgion-based BurdEn Test (REBET)
Description:

There is an increasing focus to investigate the association between rare variants and diseases. The REBET package implements the subREgion-based BurdEn Test which is a powerful burden test that simultaneously identifies susceptibility loci and sub-regions.

r-rae230acdf 2.18.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rae230acdf
Licenses: LGPL 2.0+
Synopsis: rae230acdf
Description:

This package provides a package containing an environment representing the RAE230A.CDF file.

r-rawrr 1.18.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/fgcz/rawrr/
Licenses: GPL 3
Synopsis: Direct Access to Orbitrap Data and Beyond
Description:

This package wraps the functionality of the Thermo Fisher Scientic RawFileReader .NET 8.0 assembly. Within the R environment, spectra and chromatograms are represented by S3 objects. The package provides basic functions to download and install the required third-party libraries. The package is developed, tested, and used at the Functional Genomics Center Zurich, Switzerland.

r-rolde 1.14.0
Propagated dependencies: r-summarizedexperiment@1.38.1 r-rots@2.0.0 r-rngtools@1.5.2 r-qvalue@2.40.0 r-nlme@3.1-168 r-matrixstats@1.5.0 r-foreach@1.5.2 r-dorng@1.8.6.2 r-doparallel@1.0.17
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/elolab/RolDE
Licenses: GPL 3
Synopsis: RolDE: Robust longitudinal Differential Expression
Description:

RolDE detects longitudinal differential expression between two conditions in noisy high-troughput data. Suitable even for data with a moderate amount of missing values.RolDE is a composite method, consisting of three independent modules with different approaches to detecting longitudinal differential expression. The combination of these diverse modules allows RolDE to robustly detect varying differences in longitudinal trends and expression levels in diverse data types and experimental settings.

r-runibic 1.32.0
Propagated dependencies: r-testthat@3.2.3 r-summarizedexperiment@1.38.1 r-rcpp@1.0.14 r-biclust@2.0.3.1
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: http://github.com/athril/runibic
Licenses: Expat
Synopsis: runibic: row-based biclustering algorithm for analysis of gene expression data in R
Description:

This package implements UbiBic algorithm in R. This biclustering algorithm for analysis of gene expression data was introduced by Zhenjia Wang et al. in 2016. It is currently considered the most promising biclustering method for identification of meaningful structures in complex and noisy data.

r-rqubic 1.56.0
Propagated dependencies: r-biocgenerics@0.54.0 r-biobase@2.68.0 r-biclust@2.0.3.1
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rqubic
Licenses: GPL 2
Synopsis: Qualitative biclustering algorithm for expression data analysis in R
Description:

This package implements the QUBIC algorithm introduced by Li et al. for the qualitative biclustering with gene expression data.

r-rcpi 1.46.0
Propagated dependencies: r-rlang@1.1.6 r-jsonlite@2.0.0 r-httr2@1.1.2 r-gosemsim@2.34.0 r-foreach@1.5.2 r-doparallel@1.0.17 r-curl@6.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://nanx.me/Rcpi/
Licenses: Artistic License 2.0 FSDG-compatible
Synopsis: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
Description:

This package provides a molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.

r-rain 1.44.0
Propagated dependencies: r-multtest@2.64.0 r-gmp@0.7-5
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rain
Licenses: GPL 2
Synopsis: Rhythmicity Analysis Incorporating Non-parametric Methods
Description:

This package uses non-parametric methods to detect rhythms in time series. It deals with outliers, missing values and is optimized for time series comprising 10-100 measurements. As it does not assume expect any distinct waveform it is optimal or detecting oscillating behavior (e.g. circadian or cell cycle) in e.g. genome- or proteome-wide biological measurements such as: micro arrays, proteome mass spectrometry, or metabolome measurements.

r-rvs 1.32.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RVS
Licenses: GPL 2
Synopsis: Computes estimates of the probability of related individuals sharing a rare variant
Description:

Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test).

r-rbwa 1.14.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/Jfortin1/Rbwa
Licenses: Expat
Synopsis: R wrapper for BWA-backtrack and BWA-MEM aligners
Description:

This package provides an R wrapper for BWA alignment algorithms. Both BWA-backtrack and BWA-MEM are available. Convenience function to build a BWA index from a reference genome is also provided. Currently not supported for Windows machines.

r-rcellminer 2.32.0
Propagated dependencies: r-stringr@1.5.1 r-shiny@1.10.0 r-rcellminerdata@2.32.0 r-gplots@3.2.0 r-ggplot2@3.5.2 r-biobase@2.68.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: http://discover.nci.nih.gov/cellminer/
Licenses: FSDG-compatible
Synopsis: rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
Description:

The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.

r-rsweep 1.22.0
Propagated dependencies: r-stringi@1.8.7 r-foreach@1.5.2 r-doparallel@1.0.17 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rSWeeP
Licenses: GPL 2+
Synopsis: Spaced Words Projection (SWeeP)
Description:

"Spaced Words Projection (SWeeP)" is a method for representing biological sequences using vectors preserving inter-sequence comparability.

r-regparallel 1.28.0
Propagated dependencies: r-survival@3.8-3 r-stringr@1.5.1 r-iterators@1.0.14 r-foreach@1.5.2 r-doparallel@1.0.17 r-data-table@1.17.4 r-arm@1.14-4
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/kevinblighe/RegParallel
Licenses: GPL 3
Synopsis: Standard regression functions in R enabled for parallel processing over large data-frames
Description:

In many analyses, a large amount of variables have to be tested independently against the trait/endpoint of interest, and also adjusted for covariates and confounding factors at the same time. The major bottleneck in these is the amount of time that it takes to complete these analyses. With RegParallel, a large number of tests can be performed simultaneously. On a 12-core system, 144 variables can be tested simultaneously, with 1000s of variables processed in a matter of seconds via nested parallel processing. Works for logistic regression, linear regression, conditional logistic regression, Cox proportional hazards and survival models, and Bayesian logistic regression. Also caters for generalised linear models that utilise survey weights created by the survey CRAN package and that utilise survey::svyglm'.

r-rlmm 1.72.0
Propagated dependencies: r-mass@7.3-65
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: http://www.stat.berkeley.edu/users/nrabbee/RLMM
Licenses: LGPL 2.0+
Synopsis: Genotype Calling Algorithm for Affymetrix SNP Arrays
Description:

This package provides a classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data. RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now.

r-rhesus-db0 3.22.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rhesus.db0
Licenses: Artistic License 2.0
Synopsis: Base Level Annotation databases for rhesus
Description:

Base annotation databases for rhesus, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

r-reusedata 1.10.0
Propagated dependencies: r-yaml@2.3.10 r-s4vectors@0.46.0 r-rcwlpipelines@1.26.0 r-rcwl@1.26.0 r-jsonlite@2.0.0 r-biocfilecache@2.16.0 r-basilisk@1.20.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/rworkflow/ReUseData
Licenses: GPL 3
Synopsis: Reusable and reproducible Data Management
Description:

ReUseData is an _R/Bioconductor_ software tool to provide a systematic and versatile approach for standardized and reproducible data management. ReUseData facilitates transformation of shell or other ad hoc scripts for data preprocessing into workflow-based data recipes. Evaluation of data recipes generate curated data files in their generic formats (e.g., VCF, bed). Both recipes and data are cached using database infrastructure for easy data management and reuse. Prebuilt data recipes are available through ReUseData portal ("https://rcwl.org/dataRecipes/") with full annotation and user instructions. Pregenerated data are available through ReUseData cloud bucket that is directly downloadable through "getCloudData()".

r-raexexonprobesetlocation 1.15.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RaExExonProbesetLocation
Licenses: LGPL 2.0+
Synopsis: Probe sequence data for microarrays of type RaEx
Description:

This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible.

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