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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:

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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-regutools 1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/ComunidadBioInfo/regutools
Licenses: Artistic License 2.0
Build system: r
Synopsis: regutools: an R package for data extraction from RegulonDB
Description:

RegulonDB has collected, harmonized and centralized data from hundreds of experiments for nearly two decades and is considered a point of reference for transcriptional regulation in Escherichia coli K12. Here, we present the regutools R package to facilitate programmatic access to RegulonDB data in computational biology. regutools provides researchers with the possibility of writing reproducible workflows with automated queries to RegulonDB. The regutools package serves as a bridge between RegulonDB data and the Bioconductor ecosystem by reusing the data structures and statistical methods powered by other Bioconductor packages. We demonstrate the integration of regutools with Bioconductor by analyzing transcription factor DNA binding sites and transcriptional regulatory networks from RegulonDB. We anticipate that regutools will serve as a useful building block in our progress to further our understanding of gene regulatory networks.

r-rtnduals 1.34.1
Propagated dependencies: r-rtn@2.34.1
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 identifies co-regulatory loops between pairs of regulons inferred by the RTN package by evaluating their shared target genes. It infers dual regulons and tests whether regulator pairs exhibit cooperative or competitive influences on common targets.

r-regionalpcs 1.8.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/tyeulalio/regionalpcs
Licenses: Expat
Build system: r
Synopsis: Summarizing Regional Methylation with Regional Principal Components Analysis
Description:

This package provides functions to summarize DNA methylation data using regional principal components. Regional principal components are computed using principal components analysis within genomic regions to summarize the variability in methylation levels across CpGs. The number of principal components is chosen using either the Marcenko-Pasteur or Gavish-Donoho method to identify relevant signal in the data.

r-rigvf 1.2.3
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://IGVF.github.io/rigvf
Licenses: Expat
Build system: r
Synopsis: R interface to the IGVF Catalog
Description:

The IGVF Catalog provides data on the impact of genomic variants on function. The `rigvf` package provides an interface to the IGVF Catalog, allowing easy integration with Bioconductor resources.

r-rcm 1.26.0
Propagated dependencies: r-vgam@1.1-13 r-tseries@0.10-58 r-tensor@1.5.1 r-reshape2@1.4.5 r-rcolorbrewer@1.1-3 r-phyloseq@1.54.0 r-nleqslv@3.3.5 r-mass@7.3-65 r-ggplot2@4.0.1 r-edger@4.8.0 r-alabama@2023.1.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/release/bioc/vignettes/RCM/inst/doc/RCMvignette.html/
Licenses: GPL 2
Build system: r
Synopsis: Fit row-column association models with the negative binomial distribution for the microbiome
Description:

Combine ideas of log-linear analysis of contingency table, flexible response function estimation and empirical Bayes dispersion estimation for explorative visualization of microbiome datasets. The package includes unconstrained as well as constrained analysis. In addition, diagnostic plot to detect lack of fit are available.

r-rmagpie 1.66.0
Propagated dependencies: r-pamr@1.57 r-kernlab@0.9-33 r-e1071@1.7-16 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: http://www.bioconductor.org/
Licenses: GPL 3+
Build system: r
Synopsis: MicroArray Gene-expression-based Program In Error rate estimation
Description:

Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations. A range of modern classifiers are available, including support vector machines (SVMs), nearest shrunken centroids (NSCs)... Advanced methods are provided to estimate the predictive error rate and to report the subset of genes which appear essential in discriminating between classes.

r-rguatlas4k-db 3.2.3
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rguatlas4k.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Clontech BD Atlas Long Oligos Rat 4K annotation data (chip rguatlas4k)
Description:

Clontech BD Atlas Long Oligos Rat 4K annotation data (chip rguatlas4k) assembled using data from public repositories.

r-rifi 1.14.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rifi
Licenses: FSDG-compatible
Build system: r
Synopsis: 'rifi' analyses data from rifampicin time series created by microarray or RNAseq
Description:

rifi analyses data from rifampicin time series created by microarray or RNAseq. rifi is a transcriptome data analysis tool for the holistic identification of transcription and decay associated processes. The decay constants and the delay of the onset of decay is fitted for each probe/bin. Subsequently, probes/bins of equal properties are combined into segments by dynamic programming, independent of a existing genome annotation. This allows to detect transcript segments of different stability or transcriptional events within one annotated gene. In addition to the classic decay constant/half-life analysis, rifi detects processing sites, transcription pausing sites, internal transcription start sites in operons, sites of partial transcription termination in operons, identifies areas of likely transcriptional interference by the collision mechanism and gives an estimate of the transcription velocity. All data are integrated to give an estimate of continous transcriptional units, i.e. operons. Comprehensive output tables and visualizations of the full genome result and the individual fits for all probes/bins are produced.

r-rolde 1.14.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/elolab/RolDE
Licenses: GPL 3
Build system: r
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-rqt 1.36.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/izhbannikov/rqt
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: rqt: utilities for gene-level meta-analysis
Description:

Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: "Gene-set association tests for next-generation sequencing data" by Lee et al (2016), Bioinformatics, 32(17), i611-i619, <doi:10.1093/bioinformatics/btw429>.

r-rsemmed 1.20.0
Propagated dependencies: r-stringr@1.6.0 r-magrittr@2.0.4 r-igraph@2.2.1 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/lmyint/rsemmed
Licenses: Artistic License 2.0
Build system: r
Synopsis: An interface to the Semantic MEDLINE database
Description:

This package provides a programmatic interface to the Semantic MEDLINE database. It provides functions for searching the database for concepts and finding paths between concepts. Path searching can also be tailored to user specifications, such as placing restrictions on concept types and the type of link between concepts. It also provides functions for summarizing and visualizing those paths.

r-ragene11sttranscriptcluster-db 8.8.0
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/ragene11sttranscriptcluster.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix ragene11 annotation data (chip ragene11sttranscriptcluster)
Description:

Affymetrix ragene11 annotation data (chip ragene11sttranscriptcluster) assembled using data from public repositories.

r-raex10stprobeset-db 8.8.0
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/raex10stprobeset.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix raex10 annotation data (chip raex10stprobeset)
Description:

Affymetrix raex10 annotation data (chip raex10stprobeset) assembled using data from public repositories.

r-rat2302-db 3.13.0
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rat2302.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix Rat230_2 Array annotation data (chip rat2302)
Description:

Affymetrix Affymetrix Rat230_2 Array annotation data (chip rat2302) assembled using data from public repositories.

r-ramwas 1.34.0
Propagated dependencies: r-rsamtools@2.26.0 r-kernsmooth@2.23-26 r-glmnet@4.1-10 r-genomicalignments@1.46.0 r-filematrix@1.3 r-digest@0.6.39 r-biostrings@2.78.0 r-biomart@2.66.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/ramwas/
Licenses: LGPL 3
Build system: r
Synopsis: Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Description:

This package provides a complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association analysis with respect to phenotypes of interest while correcting for top PCs and known covariates, (6) annotation of significant findings, and (7) multi-marker analysis (methylation risk score) using elastic net. Additionally, RaMWAS include tools for joint analysis of methlyation and genotype data. This work is published in Bioinformatics, Shabalin et al. (2018) <doi:10.1093/bioinformatics/bty069>.

r-rnamodr-alkanilineseq 1.24.0
Propagated dependencies: r-s4vectors@0.48.0 r-rnamodr@1.24.0 r-iranges@2.44.0 r-gviz@1.54.0 r-genomicranges@1.62.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/FelixErnst/RNAmodR.AlkAnilineSeq
Licenses: Artistic License 2.0
Build system: r
Synopsis: Detection of m7G, m3C and D modification by AlkAnilineSeq
Description:

RNAmodR.AlkAnilineSeq implements the detection of m7G, m3C and D modifications on RNA from experimental data generated with the AlkAnilineSeq protocol. The package builds on the core functionality of the RNAmodR package to detect specific patterns of the modifications in high throughput sequencing data.

r-rtn 2.34.1
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: http://dx.doi.org/10.1038/ncomms3464
Licenses: Artistic License 2.0
Build system: r
Synopsis: RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
Description:

This package provides a transcriptional regulatory network (TRN) consists of a collection of transcription factors (TFs) and the regulated target genes. TFs are regulators that recognize specific DNA sequences and guide the expression of the genome, either activating or repressing the expression the target genes. The set of genes controlled by the same TF forms a regulon. This package provides classes and methods for the reconstruction of TRNs and analysis of regulons.

r-rgug4105a-db 3.2.3
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rgug4105a.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Agilent annotation data (chip rgug4105a)
Description:

Agilent annotation data (chip rgug4105a) assembled using data from public repositories.

r-rgenometracksdata 0.99.0
Propagated dependencies: r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rGenomeTracksData
Licenses: GPL 3+
Build system: r
Synopsis: Demonstration Data from rGenomeTracks Package
Description:

rGenomeTracksData is a collection of data from pyGenomeTracks project. The purpose of this data is testing and demonstration of rGenomeTracks. This package include 14 sample file from different genomic and epigenomic file format.

r-rgraph2js 1.38.0
Propagated dependencies: r-whisker@0.4.1 r-rjson@0.2.23 r-graph@1.88.0 r-digest@0.6.39
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RGraph2js
Licenses: GPL 2
Build system: r
Synopsis: Convert a Graph into a D3js Script
Description:

Generator of web pages which display interactive network/graph visualizations with D3js, jQuery and Raphael.

r-rcwlpipelines 1.26.0
Dependencies: node@22.14.0
Propagated dependencies: r-s4vectors@0.48.0 r-rcwl@1.26.0 r-rappdirs@0.3.3 r-httr@1.4.7 r-git2r@0.36.2 r-biocfilecache@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RcwlPipelines
Licenses: GPL 2
Build system: r
Synopsis: Bioinformatics pipelines based on Rcwl
Description:

This package provides a collection of Bioinformatics tools and pipelines based on R and the Common Workflow Language.

r-ritandata 1.34.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RITANdata
Licenses: FSDG-compatible
Build system: r
Synopsis: This package contains reference annotation and network data sets
Description:

Data such as is contained in the two R data files in this package are required for the RITAN package examples. Users are highly encouraged to use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes and RITAN.md for more information, such as gathering more up-to-date annotation data.

r-rtu34cdf 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/rtu34cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: rtu34cdf
Description:

This package provides a package containing an environment representing the RT_U34.cdf file.

r-rnamodr-ml 1.24.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/FelixErnst/RNAmodR.ML
Licenses: Artistic License 2.0
Build system: r
Synopsis: Detecting patterns of post-transcriptional modifications using machine learning
Description:

RNAmodR.ML extend the functionality of the RNAmodR package and classical detection strategies towards detection through machine learning models. RNAmodR.ML provides classes, functions and an example workflow to establish a detection stratedy, which can be packaged.

Total results: 2911