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r-proteingymr 1.4.0
Propagated dependencies: r-tidyselect@1.2.1 r-tidyr@1.3.1 r-stringr@1.6.0 r-spdl@0.0.5 r-rlang@1.1.6 r-queryup@1.0.5 r-purrr@1.2.0 r-lifecycle@1.0.4 r-htmltools@0.5.8.1 r-experimenthub@3.0.0 r-dplyr@1.1.4 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/ccb-hms/ProteinGymR
Licenses: Artistic License 2.0
Build system: r
Synopsis: Programmatic access to ProteinGym datasets in R/Bioconductor
Description:

The ProteinGymR package provides analysis-ready data resources from ProteinGym, generated by Notin et al., 2023, as well as built-in functionality to visualize the data. ProteinGym comprises a collection of benchmarks for evaluating the performance of models predicting the effect of point mutations. This package provides access to 1. deep mutational scanning (DMS) scores from 217 assays measuring the impact of all possible amino acid substitutions across 186 proteins, 2. model performance metrics and prediction scores from 79 variant prediction models in the zero-shot setting and 12 models in the semi-supervised setting.

r-pd-mouse430-2 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.mouse430.2
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for The Manufacturer's Name Mouse430_2
Description:

Platform Design Info for The Manufacturer's Name Mouse430_2.

r-pd-bovine 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.bovine
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for The Manufacturer's Name Bovine
Description:

Platform Design Info for The Manufacturer's Name Bovine.

r-pd-soygene-1-1-st 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.soygene.1.1.st
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for Affymetrix SoyGene-1_1-st
Description:

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

r-pairkat 1.16.0
Propagated dependencies: r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-magrittr@2.0.4 r-keggrest@1.50.0 r-igraph@2.2.1 r-data-table@1.17.8 r-compquadform@1.4.4
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pairkat
Licenses: GPL 3
Build system: r
Synopsis: PaIRKAT
Description:

PaIRKAT is model framework for assessing statistical relationships between networks of metabolites (pathways) and an outcome of interest (phenotype). PaIRKAT queries the KEGG database to determine interactions between metabolites from which network connectivity is constructed. This model framework improves testing power on high dimensional data by including graph topography in the kernel machine regression setting. Studies on high dimensional data can struggle to include the complex relationships between variables. The semi-parametric kernel machine regression model is a powerful tool for capturing these types of relationships. They provide a framework for testing for relationships between outcomes of interest and high dimensional data such as metabolomic, genomic, or proteomic pathways. PaIRKAT uses known biological connections between high dimensional variables by representing them as edges of ‘graphs’ or ‘networks.’ It is common for nodes (e.g. metabolites) to be disconnected from all others within the graph, which leads to meaningful decreases in testing power whether or not the graph information is included. We include a graph regularization or ‘smoothing’ approach for managing this issue.

r-pd-bovgene-1-1-st 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.bovgene.1.1.st
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for Affymetrix BovGene-1_1-st
Description:

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

r-plotgardenerdata 1.16.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/PhanstielLab/plotgardenerData
Licenses: Expat
Build system: r
Synopsis: Datasets and test data files for the plotgardener package
Description:

This is a supplemental data package for the plotgardener package. Includes example datasets used in plotgardener vignettes and example raw data files. For details on how to use these datasets, see the plotgardener package vignettes.

r-pd-rae230b 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.rae230b
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for The Manufacturer's Name RAE230B
Description:

Platform Design Info for The Manufacturer's Name RAE230B.

r-pd-margene-1-1-st 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.margene.1.1.st
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for Affymetrix MarGene-1_1-st
Description:

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

r-prolocgui 2.20.0
Propagated dependencies: r-shinywidgets@0.9.0 r-shinyjs@2.1.0 r-shinyhelper@0.3.2 r-shinydashboardplus@2.0.6 r-shinydashboard@0.7.3 r-shiny@1.11.1 r-scales@1.4.0 r-proloc@1.50.0 r-msnbase@2.36.0 r-ggplot2@4.0.1 r-dt@0.34.0 r-dplyr@1.1.4 r-colourpicker@1.3.0 r-colorspace@2.1-2 r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/lgatto/pRolocGUI
Licenses: GPL 2
Build system: r
Synopsis: Interactive visualisation of spatial proteomics data
Description:

The package pRolocGUI comprises functions to interactively visualise spatial proteomics data on the basis of pRoloc, pRolocdata and shiny.

r-pd-feinberg-hg18-me-hx1 0.99.3
Propagated dependencies: r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.feinberg.hg18.me.hx1
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for NimbleGen feinberg_hg18_me_hx1
Description:

Platform Design Info for NimbleGen feinberg_hg18_me_hx1.

r-prostatecancerstockholm 1.38.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/prostateCancerStockholm
Licenses: Artistic License 2.0
Build system: r
Synopsis: Prostate Cancer Data
Description:

This package provides a Bioconductor data package for the Stockholm dataset.

r-projectr 1.26.0
Propagated dependencies: r-viridis@0.6.5 r-umap@0.2.10.0 r-tsne@0.1-3.1 r-singlecellexperiment@1.32.0 r-scales@1.4.0 r-rocr@1.0-11 r-reshape2@1.4.5 r-rcolorbrewer@1.1-3 r-nmf@0.28 r-msigdbr@25.1.1 r-matrixmodels@0.5-4 r-matrix@1.7-4 r-limma@3.66.0 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-ggalluvial@0.12.5 r-fgsea@1.36.0 r-dplyr@1.1.4 r-cowplot@1.2.0 r-cluster@2.1.8.1
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/genesofeve/projectR/
Licenses: FSDG-compatible
Build system: r
Synopsis: Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering
Description:

This package provides functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.

r-phastcons35way-ucsc-mm39 3.16.0
Propagated dependencies: r-genomicscores@2.22.0 r-annotationhub@4.0.0
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
Build system: r
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-paeg1acdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/paeg1acdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: paeg1acdf
Description:

This package provides a package containing an environment representing the Pae_G1a.CDF file.

r-pd-felgene-1-1-st 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.felgene.1.1.st
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for Affymetrix FelGene-1_1-st
Description:

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

r-pwmenrich-dmelanogaster-background 4.44.0
Propagated dependencies: r-pwmenrich@4.46.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/PWMEnrich.Dmelanogaster.background
Licenses: GPL 3
Build system: r
Synopsis: D. melanogaster background for PWMEnrich
Description:

PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs.

r-pd-vitis-vinifera 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.vitis.vinifera
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for The Manufacturer's Name Vitis_Vinifera
Description:

Platform Design Info for The Manufacturer's Name Vitis_Vinifera.

r-pd-rae230a 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.rae230a
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for The Manufacturer's Name RAE230A
Description:

Platform Design Info for The Manufacturer's Name RAE230A.

r-padma 1.20.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-multiassayexperiment@1.36.1 r-factominer@2.12
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/andreamrau/padma
Licenses: GPL 3+
Build system: r
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-pd-soygene-1-0-st 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
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
Build system: r
Synopsis: Platform Design Info for Affymetrix SoyGene-1_0-st
Description:

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

r-pd-mirna-1-0 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.mirna.1.0
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for The Manufacturer's Name miRNA-1_0
Description:

Platform Design Info for The Manufacturer's Name miRNA-1_0.

r-pd-hg-u133-plus-2 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.hg.u133.plus.2
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for The Manufacturer's Name HG-U133_Plus_2
Description:

Platform Design Info for The Manufacturer's Name HG-U133_Plus_2.

r-pd-ragene-2-1-st 3.14.1
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.ragene.2.1.st
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for Affymetrix RaGene-2_1-st
Description:

Platform Design Info for Affymetrix RaGene-2_1-st.

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Total results: 68658