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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-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-ragene21sttranscriptcluster-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/ragene21sttranscriptcluster.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix ragene21 annotation data (chip ragene21sttranscriptcluster)
Description:

Affymetrix ragene21 annotation data (chip ragene21sttranscriptcluster) assembled using data from public repositories.

r-rhesusprobe 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/rhesusprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type rhesus
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 Rhesus\_probe\_tab.

r-rnu34probe 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/rnu34probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type rnu34
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 RN-U34\_probe\_tab.

r-rcellminerdata 2.32.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rcellminerData
Licenses: FSDG-compatible
Build system: r
Synopsis: rcellminerData: Molecular Profiles and Drug Response 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-randrotation 1.22.0
Propagated dependencies: r-rdpack@2.6.4
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/phettegger/randRotation
Licenses: GPL 3
Build system: r
Synopsis: Random Rotation Methods for High Dimensional Data with Batch Structure
Description:

This package provides a collection of methods for performing random rotations on high-dimensional, normally distributed data (e.g. microarray or RNA-seq data) with batch structure. The random rotation approach allows exact testing of dependent test statistics with linear models following arbitrary batch effect correction methods.

r-rqubic 1.56.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biobase@2.70.0 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
Build system: r
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-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-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-rtopper 1.56.0
Propagated dependencies: r-multtest@2.66.0 r-limma@3.66.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RTopper
Licenses: FSDG-compatible
Build system: r
Synopsis: This package is designed to perform Gene Set Analysis across multiple genomic platforms
Description:

the RTopper package is designed to perform and integrate gene set enrichment results across multiple genomic platforms.

r-rmir-hsa 1.0.5
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/RmiR.hsa
Licenses: FSDG-compatible
Build system: r
Synopsis: Various databases of microRNA Targets
Description:

Various databases of microRNA Targets.

r-rattus-norvegicus 1.3.1
Propagated dependencies: r-txdb-rnorvegicus-ucsc-rn5-refgene@3.12.0 r-organismdbi@1.52.0 r-org-rn-eg-db@3.22.0 r-go-db@3.22.0 r-genomicfeatures@1.62.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/Rattus.norvegicus
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for the Rattus.norvegicus object
Description:

This package contains the Rattus.norvegicus object to access data from several related annotation packages.

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
Build system: r
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-rgu34a-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/rgu34a.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix RG_U34A Array annotation data (chip rgu34a)
Description:

Affymetrix Affymetrix RG_U34A Array annotation data (chip rgu34a) assembled using data from public repositories.

r-rgu34b-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/rgu34b.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix RG_U34B Array annotation data (chip rgu34b)
Description:

Affymetrix Affymetrix RG_U34B Array annotation data (chip rgu34b) assembled using data from public repositories.

r-ruvcorr 1.42.0
Propagated dependencies: r-snowfall@1.84-6.3 r-reshape2@1.4.5 r-psych@2.5.6 r-mass@7.3-65 r-lattice@0.22-7 r-gridextra@2.3 r-corrplot@0.95 r-bladderbatch@1.48.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RUVcorr
Licenses: GPL 2
Build system: r
Synopsis: Removal of unwanted variation for gene-gene correlations and related analysis
Description:

RUVcorr allows to apply global removal of unwanted variation (ridged version of RUV) to real and simulated gene expression data.

r-raids 1.8.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://krasnitzlab.github.io/RAIDS/
Licenses: FSDG-compatible
Build system: r
Synopsis: Robust Ancestry Inference using Data Synthesis
Description:

This package implements specialized algorithms that enable genetic ancestry inference from various cancer sequences sources (RNA, Exome and Whole-Genome sequences). This package also implements a simulation algorithm that generates synthetic cancer-derived data. This code and analysis pipeline was designed and developed for the following publication: Belleau, P et al. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.

r-ribodipa 1.18.0
Propagated dependencies: r-txdbmaker@1.6.0 r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-reldist@1.7-2 r-rcpp@1.1.0 r-qvalue@2.42.0 r-matrixstats@1.5.0 r-iranges@2.44.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomicalignments@1.46.0 r-foreach@1.5.2 r-elitism@1.1.1 r-doparallel@1.0.17 r-deseq2@1.50.2 r-data-table@1.17.8 r-biocgenerics@0.56.0 r-biocfilecache@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RiboDiPA
Licenses: LGPL 3+
Build system: r
Synopsis: Differential pattern analysis for Ribo-seq data
Description:

This package performs differential pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and footprint visualization.

r-randpack 1.56.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/randPack
Licenses: FSDG-compatible
Build system: r
Synopsis: Randomization routines for Clinical Trials
Description:

This package provides a suite of classes and functions for randomizing patients in clinical trials.

r-roastgsa 1.8.0
Propagated dependencies: r-rcolorbrewer@1.1-3 r-limma@3.66.0 r-gplots@3.2.0 r-ggplot2@4.0.1 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/roastgsa
Licenses: GPL 3
Build system: r
Synopsis: Rotation based gene set analysis
Description:

This package implements a variety of functions useful for gene set analysis using rotations to approximate the null distribution. It contributes with the implementation of seven test statistic scores that can be used with different goals and interpretations. Several functions are available to complement the statistical results with graphical representations.

r-regionreport 1.44.0
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-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-rae230bprobe 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/rae230bprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type rae230b
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 RAE230B\_probe\_tab.

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.

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Total results: 69112