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    / / /\ \ \ / / /  \ \_\\ \ \_/      \ \ \ \/___/
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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-rrdp 1.44.0
Propagated dependencies: r-rjava@1.0-11 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/mhahsler/rRDP/
Licenses: FSDG-compatible
Build system: r
Synopsis: Interface to the RDP Classifier
Description:

This package installs and interfaces the naive Bayesian classifier for 16S rRNA sequences developed by the Ribosomal Database Project (RDP). With this package the classifier trained with the standard training set can be used or a custom classifier can be trained.

r-rcx 1.14.1
Propagated dependencies: r-plyr@1.8.9 r-jsonlite@2.0.0 r-igraph@2.2.1
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/frankkramer-lab/RCX
Licenses: Expat
Build system: r
Synopsis: R package implementing the Cytoscape Exchange (CX) format
Description:

Create, handle, validate, visualize and convert networks in the Cytoscape exchange (CX) format to standard data types and objects. The package also provides conversion to and from objects of iGraph and graphNEL. The CX format is also used by the NDEx platform, a online commons for biological networks, and the network visualization software Cytocape.

r-rbiopaxparser 2.50.0
Propagated dependencies: r-xml@3.99-0.20 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/frankkramer-lab/rBiopaxParser
Licenses: GPL 2+
Build system: r
Synopsis: Parses BioPax files and represents them in R
Description:

Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported.

r-retrofit 1.10.0
Propagated dependencies: r-rcpp@1.1.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/qunhualilab/retrofit
Licenses: GPL 3
Build system: r
Synopsis: RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics
Description:

RETROFIT is a Bayesian non-negative matrix factorization framework to decompose cell type mixtures in ST data without using external single-cell expression references. RETROFIT outperforms existing reference-based methods in estimating cell type proportions and reconstructing gene expressions in simulations with varying spot size and sample heterogeneity, irrespective of the quality or availability of the single-cell reference. RETROFIT recapitulates known cell-type localization patterns in a Slide-seq dataset of mouse cerebellum without using any single-cell data.

r-rhesuscdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rhesuscdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: rhesuscdf
Description:

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

r-rtpca 1.20.0
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.3.0 r-proc@1.19.0.1 r-ggplot2@4.0.1 r-fdrtool@1.2.18 r-dplyr@1.1.4 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/Rtpca
Licenses: GPL 3
Build system: r
Synopsis: Thermal proximity co-aggregation with R
Description:

R package for performing thermal proximity co-aggregation analysis with thermal proteome profiling datasets to analyse protein complex assembly and (differential) protein-protein interactions across conditions.

r-rseqan 1.30.0
Propagated dependencies: r-rcpp@1.1.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RSeqAn
Licenses: Modified BSD
Build system: r
Synopsis: R SeqAn
Description:

Headers and some wrapper functions from the SeqAn C++ library for ease of usage in R.

r-regionreport 1.44.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rmarkdown@2.30 r-refmanager@1.4.0 r-knitrbootstrap@1.0.3 r-knitr@1.50 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-deseq2@1.50.2 r-derfinder@1.44.0 r-deformats@1.38.0 r-biocstyle@2.38.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/leekgroup/regionReport
Licenses: Artistic License 2.0
Build system: r
Synopsis: Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Description:

Generate HTML or PDF reports to explore a set of regions such as the results from annotation-agnostic expression analysis of RNA-seq data at base-pair resolution performed by derfinder. You can also create reports for DESeq2 or edgeR results.

r-rtrm 1.48.0
Propagated dependencies: r-rsqlite@2.4.4 r-igraph@2.2.1 r-dbi@1.2.3 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/ddiez/rTRM
Licenses: GPL 3
Build system: r
Synopsis: Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks
Description:

rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.

r-rcsl 1.18.0
Propagated dependencies: r-umap@0.2.10.0 r-singlecellexperiment@1.32.0 r-rtsne@0.17 r-rcppannoy@0.0.22 r-rcpp@1.1.0 r-pracma@2.4.6 r-nbclust@3.0.1 r-matrixgenerics@1.22.0 r-igraph@2.2.1 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/QinglinMei/RCSL
Licenses: Artistic License 2.0
Build system: r
Synopsis: Rank Constrained Similarity Learning for single cell RNA sequencing data
Description:

This package provides a novel clustering algorithm and toolkit RCSL (Rank Constrained Similarity Learning) to accurately identify various cell types using scRNA-seq data from a complex tissue. RCSL considers both lo-cal similarity and global similarity among the cells to discern the subtle differences among cells of the same type as well as larger differences among cells of different types. RCSL uses Spearman’s rank correlations of a cell’s expression vector with those of other cells to measure its global similar-ity, and adaptively learns neighbour representation of a cell as its local similarity. The overall similar-ity of a cell to other cells is a linear combination of its global similarity and local similarity.

r-rucova 1.2.0
Propagated dependencies: r-tidyverse@2.0.0 r-tidyr@1.3.1 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-singlecellexperiment@1.32.0 r-s4vectors@0.48.0 r-matrix@1.7-4 r-magrittr@2.0.4 r-ggplot2@4.0.1 r-fastdummies@1.7.5 r-dplyr@1.1.4 r-complexheatmap@2.26.0 r-circlize@0.4.16
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/molsysbio/RUCova
Licenses: GPL 3
Build system: r
Synopsis: Removes unwanted covariance from mass cytometry data
Description:

Mass cytometry enables the simultaneous measurement of dozens of protein markers at the single-cell level, producing high dimensional datasets that provide deep insights into cellular heterogeneity and function. However, these datasets often contain unwanted covariance introduced by technical variations, such as differences in cell size, staining efficiency, and instrument-specific artifacts, which can obscure biological signals and complicate downstream analysis. This package addresses this challenge by implementing a robust framework of linear models designed to identify and remove these sources of unwanted covariance. By systematically modeling and correcting for technical noise, the package enhances the quality and interpretability of mass cytometry data, enabling researchers to focus on biologically relevant signals.

r-rgenometracks 1.16.0
Propagated dependencies: r-rgenometracksdata@0.99.0 r-reticulate@1.44.1 r-imager@1.0.5
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rGenomeTracks
Licenses: GPL 3
Build system: r
Synopsis: Integerated visualization of epigenomic data
Description:

rGenomeTracks package leverages the power of pyGenomeTracks software with the interactivity of R. pyGenomeTracks is a python software that offers robust method for visualizing epigenetic data files like narrowPeak, Hic matrix, TADs and arcs, however though, here is no way currently to use it within R interactive session. rGenomeTracks wrapped the whole functionality of pyGenomeTracks with additional utilites to make to more pleasant for R users.

r-rfarm 1.22.0
Propagated dependencies: r-xml2@1.5.0 r-stringi@1.8.7 r-s4vectors@0.48.0 r-rvest@1.0.5 r-rsvg@2.7.0 r-magick@2.9.0 r-jsonlite@2.0.0 r-iranges@2.44.0 r-httr@1.4.7 r-data-table@1.17.8 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rfaRm
Licenses: GPL 3
Build system: r
Synopsis: An R interface to the Rfam database
Description:

rfaRm provides a client interface to the Rfam database of RNA families. Data that can be retrieved include RNA families, secondary structure images, covariance models, sequences within each family, alignments leading to the identification of a family and secondary structures in the dot-bracket format.

r-rae230bcdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rae230bcdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: rae230bcdf
Description:

This package provides a package containing an environment representing the RAE230B.CDF file.

r-rat2302cdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rat2302cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: rat2302cdf
Description:

This package provides a package containing an environment representing the Rat230_2.cdf file.

r-rtcga-clinical 20151101.40.0
Propagated dependencies: r-rtcga@1.40.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RTCGA.clinical
Licenses: GPL 2
Build system: r
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-rfpred 1.48.0
Propagated dependencies: r-seqinfo@1.0.0 r-rsamtools@2.26.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rfPred
Licenses: FSDG-compatible
Build system: r
Synopsis: Assign rfPred functional prediction scores to a missense variants list
Description:

Based on external numerous data files where rfPred scores are pre-calculated on all genomic positions of the human exome, the package gives rfPred scores to missense variants identified by the chromosome, the position (hg19 version), the referent and alternative nucleotids and the uniprot identifier of the protein. Note that for using the package, the user has to download the TabixFile and index (approximately 3.3 Go).

r-rnbeads-hg38 1.42.1
Propagated dependencies: r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RnBeads.hg38
Licenses: GPL 3
Build system: r
Synopsis: RnBeads.hg38
Description:

RnBeads annotation package for the assembly hg38.

r-rtnduals 1.34.0
Propagated dependencies: r-rtn@2.34.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RTNduals
Licenses: Artistic License 2.0
Build system: r
Synopsis: Analysis of co-regulation and inference of 'dual regulons'
Description:

RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer dual regulons', a new concept that tests whether regulators can co-operate or compete in influencing targets.

r-rawdiag 1.6.0
Propagated dependencies: r-shiny@1.11.1 r-scales@1.4.0 r-rlang@1.1.6 r-reshape2@1.4.5 r-rawrr@1.18.0 r-htmltools@0.5.8.1 r-hexbin@1.28.5 r-ggplot2@4.0.1 r-dplyr@1.1.4 r-biocparallel@1.44.0 r-biocmanager@1.30.27
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/fgcz/rawDiag/
Licenses: GPL 3
Build system: r
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-rat2302frmavecs 0.99.11
Propagated dependencies: r-frma@1.62.0 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rat2302frmavecs
Licenses: GPL 2+
Build system: r
Synopsis: Vectors used by frma for microarrays of type rat2302rnentrezg
Description:

This package was created with the help of frmaTools version 1.24.0.

r-regenrich 1.20.0
Propagated dependencies: r-wgcna@1.73 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-reshape2@1.4.5 r-randomforest@4.7-1.2 r-magrittr@2.0.4 r-limma@3.66.0 r-ggplot2@4.0.1 r-fgsea@1.36.0 r-dplyr@1.1.4 r-dose@4.4.0 r-deseq2@1.50.2 r-biocstyle@2.38.0 r-biocset@1.24.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RegEnrich
Licenses: GPL 2+
Build system: r
Synopsis: Gene regulator enrichment analysis
Description:

This package is a pipeline to identify the key gene regulators in a biological process, for example in cell differentiation and in cell development after stimulation. There are four major steps in this pipeline: (1) differential expression analysis; (2) regulator-target network inference; (3) enrichment analysis; and (4) regulators scoring and ranking.

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+
Build system: r
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-rnaseqpower 1.50.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RNASeqPower
Licenses: FSDG-compatible
Build system: r
Synopsis: Sample size for RNAseq studies
Description:

RNA-seq, sample size.

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Total results: 68655