_            _    _        _         _
      /\ \         /\ \ /\ \     /\_\      / /\
      \_\ \       /  \ \\ \ \   / / /     / /  \
      /\__ \     / /\ \ \\ \ \_/ / /     / / /\ \__
     / /_ \ \   / / /\ \ \\ \___/ /     / / /\ \___\
    / / /\ \ \ / / /  \ \_\\ \ \_/      \ \ \ \/___/
   / / /  \/_// / /   / / / \ \ \        \ \ \
  / / /      / / /   / / /   \ \ \   _    \ \ \
 / / /      / / /___/ / /     \ \ \ /_/\__/ / /
/_/ /      / / /____\/ /       \ \_\\ \/___/ /
\_\/       \/_________/         \/_/ \_____\/

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-pd-hg-u95av2 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.hg.u95av2
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for The Manufacturer's Name HG_U95Av2
Description:

Platform Design Info for The Manufacturer's Name HG_U95Av2.

r-pd-soygene-1-0-st 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.soygene.1.0.st
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for Affymetrix SoyGene-1_0-st
Description:

Platform Design Info for Affymetrix SoyGene-1_0-st.

r-pd-medgene-1-1-st 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.medgene.1.1.st
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for Affymetrix MedGene-1_1-st
Description:

Platform Design Info for Affymetrix MedGene-1_1-st.

r-pd-rn-u34 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.rn.u34
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for The Manufacturer's Name RN_U34
Description:

Platform Design Info for The Manufacturer's Name RN_U34.

r-pd-ovigene-1-0-st 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.ovigene.1.0.st
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for Affymetrix OviGene-1_0-st
Description:

Platform Design Info for Affymetrix OviGene-1_0-st.

r-paa 1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: http://www.ruhr-uni-bochum.de/mpc/software/PAA/
Licenses: Modified BSD
Synopsis: PAA (Protein Array Analyzer)
Description:

PAA imports single color (protein) microarray data that has been saved in gpr file format - esp. ProtoArray data. After preprocessing (background correction, batch filtering, normalization) univariate feature preselection is performed (e.g., using the "minimum M statistic" approach - hereinafter referred to as "mMs"). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Therefore, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation.

r-pharmacogx 3.14.0
Propagated dependencies: r-summarizedexperiment@1.38.1 r-s4vectors@0.46.0 r-reshape2@1.4.4 r-rcpp@1.0.14 r-rcolorbrewer@1.1-3 r-multiassayexperiment@1.34.0 r-magicaxis@2.4.5 r-jsonlite@2.0.0 r-ggplot2@3.5.2 r-downloader@0.4.1 r-data-table@1.17.4 r-coregx@2.12.0 r-coop@0.6-3 r-checkmate@2.3.2 r-catools@1.18.3 r-boot@1.3-31 r-biocparallel@1.42.0 r-biocgenerics@0.54.0 r-biobase@2.68.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/PharmacoGx
Licenses: GPL 3+
Synopsis: Analysis of Large-Scale Pharmacogenomic Data
Description:

This package contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.

r-pepsnmrdata 1.28.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/PepsNMRData
Licenses: GPL 2 FSDG-compatible
Synopsis: Datasets for the PepsNMR package
Description:

This package contains all the datasets used in the PepsNMR package.

r-pd-zebrafish 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.zebrafish
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for The Manufacturer's Name Zebrafish
Description:

Platform Design Info for The Manufacturer's Name Zebrafish.

r-padma 1.20.0
Propagated dependencies: r-summarizedexperiment@1.38.1 r-s4vectors@0.46.0 r-multiassayexperiment@1.34.0 r-factominer@2.11
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/andreamrau/padma
Licenses: GPL 3+
Synopsis: Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
Description:

Use multiple factor analysis to calculate individualized pathway-centric scores of deviation with respect to the sampled population based on multi-omic assays (e.g., RNA-seq, copy number alterations, methylation, etc). Graphical and numerical outputs are provided to identify highly aberrant individuals for a particular pathway of interest, as well as the gene and omics drivers of aberrant multi-omic profiles.

r-phastcons35way-ucsc-mm39 3.16.0
Propagated dependencies: r-genomicscores@2.20.0 r-annotationhub@3.16.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/phastCons35way.UCSC.mm39
Licenses: Artistic License 2.0
Synopsis: UCSC phastCons mm39 conservation scores AnnotationHub Resource Metadata
Description:

Store UCSC phastCons mm39 conservation scores AnnotationHub Resource Metadata. Provide provenance and citation information for UCSC phastCons mm39 conservation score AnnotationHub resources. Illustrate in a vignette how to access those resources.

r-ptairdata 1.18.0
Propagated dependencies: r-signal@1.8-1 r-rhdf5@2.52.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/ptairData
Licenses: GPL 3
Synopsis: PTR-TOF-MS volatolomics raw datasets from exhaled air and cell culture headspace
Description:

The package ptairData contains two raw datasets from Proton-Transfer-Reaction Time-of-Flight mass spectrometer acquisitions (PTR-TOF-MS), in the HDF5 format. One from the exhaled air of two volunteer healthy individuals with three replicates, and one from the cell culture headspace from two mycobacteria species and one control (culture medium only) with two replicates. Those datasets are used in the examples and in the vignette of the ptairMS package (PTR-TOF-MS data pre-processing). There are also used to gererate the ptrSet in the ptairMS data : exhaledPtrset and mycobacteriaSet.

r-pepsettest 1.4.0
Propagated dependencies: r-tibble@3.2.1 r-summarizedexperiment@1.38.1 r-reshape2@1.4.4 r-matrixstats@1.5.0 r-mass@7.3-65 r-lme4@1.1-37 r-limma@3.64.1 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/JmWangBio/PepSetTest
Licenses: GPL 3+
Synopsis: Peptide Set Test
Description:

Peptide Set Test (PepSetTest) is a peptide-centric strategy to infer differentially expressed proteins in LC-MS/MS proteomics data. This test detects coordinated changes in the expression of peptides originating from the same protein and compares these changes against the rest of the peptidome. Compared to traditional aggregation-based approaches, the peptide set test demonstrates improved statistical power, yet controlling the Type I error rate correctly in most cases. This test can be valuable for discovering novel biomarkers and prioritizing drug targets, especially when the direct application of statistical analysis to protein data fails to provide substantial insights.

r-phylop35way-ucsc-mm39 3.16.0
Propagated dependencies: r-genomicscores@2.20.0 r-annotationhub@3.16.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/phyloP35way.UCSC.mm39
Licenses: Artistic License 2.0
Synopsis: UCSC phyloP mm39 conservation scores AnnotationHub Resource Metadata
Description:

Store UCSC phyloP mm39 conservation scores AnnotationHub Resource Metadata. Provide provenance and citation information for UCSC phyloP mm39 conservation score AnnotationHub resources. Illustrate in a vignette how to access those resources.

r-paircompviz 1.48.0
Propagated dependencies: r-rgraphviz@2.52.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/paircompviz
Licenses: FSDG-compatible
Synopsis: Multiple comparison test visualization
Description:

This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized as nodes in Hasse diagram. Such approach enables very clear and vivid depiction of which group is significantly greater than which others, especially if comparing a large number of groups.

r-pd-mg-u74av2 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.mg.u74av2
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for The Manufacturer's Name MG_U74Av2
Description:

Platform Design Info for The Manufacturer's Name MG_U74Av2.

r-pd-mogene-2-0-st 3.14.1
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.mogene.2.0.st
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for Affymetrix MoGene-2_0-st
Description:

Platform Design Info for Affymetrix MoGene-2_0-st.

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

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

r-pd-rg-u34c 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.rg.u34c
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for The Manufacturer's Name RG_U34C
Description:

Platform Design Info for The Manufacturer's Name RG_U34C.

r-pathwaypca 1.26.0
Propagated dependencies: r-survival@3.8-3 r-lars@1.3
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: <https://gabrielodom.github.io/pathwayPCA/>
Licenses: GPL 3
Synopsis: Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Description:

pathwayPCA is an integrative analysis tool that implements the principal component analysis (PCA) based pathway analysis approaches described in Chen et al. (2008), Chen et al. (2010), and Chen (2011). pathwayPCA allows users to: (1) Test pathway association with binary, continuous, or survival phenotypes. (2) Extract relevant genes in the pathways using the SuperPCA and AES-PCA approaches. (3) Compute principal components (PCs) based on the selected genes. These estimated latent variables represent pathway activities for individual subjects, which can then be used to perform integrative pathway analysis, such as multi-omics analysis. (4) Extract relevant genes that drive pathway significance as well as data corresponding to these relevant genes for additional in-depth analysis. (5) Perform analyses with enhanced computational efficiency with parallel computing and enhanced data safety with S4-class data objects. (6) Analyze studies with complex experimental designs, with multiple covariates, and with interaction effects, e.g., testing whether pathway association with clinical phenotype is different between male and female subjects. Citations: Chen et al. (2008) <https://doi.org/10.1093/bioinformatics/btn458>; Chen et al. (2010) <https://doi.org/10.1002/gepi.20532>; and Chen (2011) <https://doi.org/10.2202/1544-6115.1697>.

r-pd-rg-u34b 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.rg.u34b
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for The Manufacturer's Name RG_U34B
Description:

Platform Design Info for The Manufacturer's Name RG_U34B.

r-pd-guigene-1-0-st 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.guigene.1.0.st
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for Affymetrix GuiGene-1_0-st
Description:

Platform Design Info for Affymetrix GuiGene-1_0-st.

r-pd-mu11ksubb 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.mu11ksubb
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for The Manufacturer's Name Mu11KsubB
Description:

Platform Design Info for The Manufacturer's Name Mu11KsubB.

r-pairedgsea 1.10.0
Propagated dependencies: r-sva@3.56.0 r-summarizedexperiment@1.38.1 r-showtext@0.9-7 r-s4vectors@0.46.0 r-msigdbr@24.1.0 r-limma@3.64.1 r-ggplot2@3.5.2 r-fgsea@1.34.0 r-dexseq@1.54.1 r-deseq2@1.48.1 r-biocparallel@1.42.0 r-aggregation@1.0.1
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/shdam/pairedGSEA
Licenses: Expat
Synopsis: Paired DGE and DGS analysis for gene set enrichment analysis
Description:

pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes with a wrapper function for running an Over-Representation Analysis (ORA) and functionalities for plotting the results.

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Total results: 45109