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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-qvalue 2.42.0
Propagated dependencies: r-ggplot2@4.0.1 r-reshape2@1.4.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/StoreyLab/qvalue
Licenses: LGPL 3+
Build system: r
Synopsis: Q-value estimation for false discovery rate control
Description:

This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local false discovery rate (FDR) values. The q-value of a test measures the proportion of false positives incurred when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

r-assessorf 1.28.0
Propagated dependencies: r-biostrings@2.78.0 r-decipher@3.6.0 r-genomicranges@1.62.0 r-iranges@2.44.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AssessORF
Licenses: GPL 3
Build system: r
Synopsis: Assess gene predictions using proteomics and evolutionary conservation
Description:

In order to assess the quality of a set of predicted genes for a genome, evidence must first be mapped to that genome. Next, each gene must be categorized based on how strong the evidence is for or against that gene. The AssessORF package provides the functions and class structures necessary for accomplishing those tasks, using proteomics hits and evolutionarily conserved start codons as the forms of evidence.

r-alpsnmr 4.12.0
Propagated dependencies: r-baseline@1.3-7 r-biocparallel@1.44.0 r-cli@3.6.5 r-dplyr@1.1.4 r-fs@1.6.6 r-generics@0.1.4 r-ggplot2@4.0.1 r-glue@1.8.0 r-htmltools@0.5.8.1 r-magrittr@2.0.4 r-matrixstats@1.5.0 r-mixomics@6.34.0 r-pcapp@2.0-5 r-purrr@1.2.0 r-readxl@1.4.5 r-reshape2@1.4.5 r-rlang@1.1.6 r-rmarkdown@2.30 r-scales@1.4.0 r-signal@1.8-1 r-speaq@2.7.0 r-stringr@1.6.0 r-tibble@3.3.0 r-tidyr@1.3.1 r-tidyselect@1.2.1 r-vctrs@0.6.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://sipss.github.io/AlpsNMR/
Licenses: Expat
Build system: r
Synopsis: Automated spectral processing system for NMR
Description:

This package reads Bruker NMR data directories both zipped and unzipped. It provides automated and efficient signal processing for untargeted NMR metabolomics. It is able to interpolate the samples, detect outliers, exclude regions, normalize, detect peaks, align the spectra, integrate peaks, manage metadata and visualize the spectra. After spectra processing, it can apply multivariate analysis on extracted data. Efficient plotting with 1-D data is also available. Basic reading of 1D ACD/Labs exported JDX samples is also available.

r-maftools 2.26.0
Propagated dependencies: r-data-table@1.17.8 r-dnacopy@1.84.0 r-pheatmap@1.0.13 r-rcolorbrewer@1.1-3 r-rhtslib@3.6.0 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/PoisonAlien/maftools
Licenses: Expat
Build system: r
Synopsis: Summarize, analyze and visualize MAF files
Description:

Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.

r-slingshot 2.18.0
Propagated dependencies: r-igraph@2.2.1 r-matrixstats@1.5.0 r-princurve@2.1.6 r-s4vectors@0.48.0 r-singlecellexperiment@1.32.0 r-summarizedexperiment@1.40.0 r-trajectoryutils@1.18.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/slingshot
Licenses: Artistic License 2.0
Build system: r
Synopsis: Tools for ordering single-cell sequencing
Description:

This package provides functions for inferring continuous, branching lineage structures in low-dimensional data. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.

r-fdb-infiniummethylation-hg19 2.2.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biostrings@2.78.0 r-genomicfeatures@1.62.0 r-org-hs-eg-db@3.22.0 r-txdb-hsapiens-ucsc-hg19-knowngene@3.22.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Compiled HumanMethylation27 and HumanMethylation450 annotations
Description:

This is an annotation package for Illumina Infinium DNA methylation probes. It contains the compiled HumanMethylation27 and HumanMethylation450 annotations.

r-bionet 1.70.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biobase@2.70.0 r-graph@1.88.0 r-igraph@2.2.1 r-rbgl@1.86.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://bioconductor.org/packages/release/bioc/html/BioNet.html
Licenses: GPL 2+
Build system: r
Synopsis: Functional analysis of biological networks
Description:

This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.

r-absfiltergsea 1.5.1
Propagated dependencies: r-biobase@2.70.0 r-deseq@1.39.0 r-limma@3.66.0 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/web/packages/AbsFilterGSEA/
Licenses: GPL 2
Build system: r
Synopsis: Improved false positive control of gene-permuting with absolute filtering
Description:

This package provides a function that performs gene-permuting of a gene-set enrichment analysis (GSEA) calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.

r-bayseq 2.44.0
Propagated dependencies: r-abind@1.4-8 r-edger@4.8.0 r-genomicranges@1.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/baySeq/
Licenses: GPL 3
Build system: r
Synopsis: Bayesian analysis of differential expression patterns in count data
Description:

This package identifies differential expression in high-throughput count data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.

r-a4reporting 1.58.0
Propagated dependencies: r-xtable@1.8-4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/a4Reporting/
Licenses: GPL 3
Build system: r
Synopsis: Automated Affymetrix array analysis reporting package
Description:

This is a package for the automated analysis of Affymetrix arrays. It provides reporting features.

r-annaffy 1.82.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biobase@2.70.0 r-biocmanager@1.30.27 r-dbi@1.2.3 r-go-db@3.22.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/annaffy/
Licenses: LGPL 2.1+
Build system: r
Synopsis: Annotation tools for Affymetrix biological metadata
Description:

This package provides functions for handling data from Bioconductor Affymetrix annotation data packages. It produces compact HTML and text reports including experimental data and URL links to many online databases. It allows searching of biological metadata using various criteria.

r-breakpointr 1.28.0
Propagated dependencies: r-biocgenerics@0.56.0 r-breakpointrdata@1.28.0 r-cowplot@1.2.0 r-doparallel@1.0.17 r-foreach@1.5.2 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-gtools@3.9.5 r-iranges@2.44.0 r-rsamtools@2.26.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/daewoooo/BreakPointR
Licenses: Expat
Build system: r
Synopsis: Find breakpoints in Strand-seq data
Description:

This package implements functions for finding breakpoints, plotting and export of Strand-seq data.

r-bsgenome-mmusculus-ucsc-mm9 1.4.0
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Mouse
Description:

This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, July 2007) and stored in Biostrings objects.

r-acde 1.40.0
Propagated dependencies: r-boot@1.3-32
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/acde
Licenses: GPL 3
Build system: r
Synopsis: Identification of differentially expressed genes with artificial components
Description:

This package provides a multivariate inferential analysis method for detecting differentially expressed genes in gene expression data. It uses artificial components, close to the data's principal components but with an exact interpretation in terms of differential genetic expression, to identify differentially expressed genes while controlling the false discovery rate (FDR).

r-biotip 1.24.0
Propagated dependencies: r-cluster@2.1.8.1 r-doparallel@1.0.17 r-foreach@1.5.2 r-genomicranges@1.62.0 r-igraph@2.2.1 r-mass@7.3-65 r-psych@2.5.6 r-scran@1.38.0 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/xyang2uchicago/BioTIP
Licenses: GPL 2
Build system: r
Synopsis: R package for characterization of biological tipping-point
Description:

This package adopts tipping-point theory to transcriptome profiles to help unravel disease regulatory trajectory.

r-mast 1.36.0
Propagated dependencies: r-abind@1.4-8 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-data-table@1.17.8 r-ggplot2@4.0.1 r-matrix@1.7-4 r-plyr@1.8.9 r-progress@1.2.3 r-reshape2@1.4.5 r-s4vectors@0.48.0 r-singlecellexperiment@1.32.0 r-stringr@1.6.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/RGLab/MAST/
Licenses: GPL 2+
Build system: r
Synopsis: Model-based analysis of single cell transcriptomics
Description:

This package provides methods and models for handling zero-inflated single cell assay data.

r-simpleaffy 2.66.0
Propagated dependencies: r-affy@1.88.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-gcrma@2.82.0 r-genefilter@1.92.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/simpleaffy/
Licenses: GPL 2+
Build system: r
Synopsis: Very simple high level analysis of Affymetrix data
Description:

This package provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy use of the affy library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures.

r-activedriverwgs 1.2.0
Propagated dependencies: r-biostrings@2.78.0 r-bsgenome@1.78.0 r-bsgenome-hsapiens-ucsc-hg19@1.4.3 r-bsgenome-hsapiens-ucsc-hg38@1.4.5 r-bsgenome-mmusculus-ucsc-mm9@1.4.0 r-bsgenome-mmusculus-ucsc-mm10@1.4.3 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/web/packages/ActiveDriverWGS/
Licenses: GPL 3
Build system: r
Synopsis: Driver discovery tool for cancer whole genomes
Description:

This package provides a method for finding an enrichment of cancer simple somatic mutations (SNVs and Indels) in functional elements across the human genome. ActiveDriverWGS detects coding and noncoding driver elements using whole genome sequencing data.

r-r3cseq 1.56.0
Propagated dependencies: r-biostrings@2.78.0 r-data-table@1.17.8 r-genomicranges@1.62.0 r-iranges@2.44.0 r-qvalue@2.42.0 r-rcolorbrewer@1.1-3 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-seqinfo@1.0.0 r-sqldf@0.4-11 r-vgam@1.1-13
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://r3cseq.genereg.net/Site/index.html
Licenses: GPL 3
Build system: r
Synopsis: Analysis of Chromosome conformation capture and Next-generation sequencing
Description:

This package is used for the analysis of long-range chromatin interactions from 3C-seq assay.

r-abadata 1.12.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/ABAData/
Licenses: GPL 2+
Build system: r
Synopsis: Gene expression in human brain regions from Allen Brain Atlas
Description:

This package provides the data for the gene expression enrichment analysis conducted in the package ABAEnrichment. The package includes three datasets which are derived from the Allen Brain Atlas:

  1. Gene expression data from Human Brain (adults) averaged across donors,

  2. Gene expression data from the Developing Human Brain pooled into five age categories and averaged across donors, and

  3. a developmental effect score based on the Developing Human Brain expression data.

All datasets are restricted to protein coding genes.

r-copywriter 2.29.0
Propagated dependencies: r-biocparallel@1.44.0 r-chipseq@1.60.0 r-copyhelper@1.42.0 r-data-table@1.17.8 r-dnacopy@1.84.0 r-futile-logger@1.4.3 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-gtools@3.9.5 r-iranges@2.44.0 r-matrixstats@1.5.0 r-rsamtools@2.26.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/PeeperLab/CopywriteR
Licenses: GPL 2
Build system: r
Synopsis: Copy number information from targeted sequencing
Description:

CopywriteR extracts DNA copy number information from targeted sequencing by utilizing off-target reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.

r-graphite 1.56.0
Propagated dependencies: r-annotationdbi@1.72.0 r-dir-expiry@1.18.0 r-graph@1.88.0 r-httr@1.4.7 r-lifecycle@1.0.4 r-purrr@1.2.0 r-rappdirs@0.3.3 r-rlang@1.1.6
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/graphite/
Licenses: AGPL 3+
Build system: r
Synopsis: Networks from pathway databases
Description:

Graphite provides networks derived from eight public pathway databases, and automates the conversion of node identifiers (e.g. from Entrez IDs to gene symbols).

r-dsb 2.0.1
Propagated dependencies: r-limma@3.66.0 r-magrittr@2.0.4 r-mclust@6.1.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/niaid/dsb
Licenses: CC0
Build system: r
Synopsis: Normalize & denoise droplet single cell protein data (CITE-Seq)
Description:

R-dsb improves protein expression analysis in droplet-based single-cell studies. The package specifically addresses noise in raw protein UMI counts from methods like CITE-seq. It identifies and removes two main sources of noise—protein-specific noise from unbound antibodies and droplet/cell-specific noise. The package is applicable to various methods, including CITE-seq, REAP-seq, ASAP-seq, TEA-seq, and Mission Bioplatform data. Check the vignette for tutorials on integrating dsb with Seurat and Bioconductor, and using dsb in Python.

r-mzid 1.48.0
Propagated dependencies: r-doparallel@1.0.17 r-foreach@1.5.2 r-iterators@1.0.14 r-plyr@1.8.9 r-protgenerics@1.42.0 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/mzID
Licenses: GPL 2+
Build system: r
Synopsis: Parser for mzIdentML files
Description:

This package provides a parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less pretty output than a vendor specific parser.

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