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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.

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r-pd-hg18-60mer-expr 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.hg18.60mer.expr
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for NimbleGen hg18_60mer_expr
Description:

Platform Design Info for NimbleGen hg18_60mer_expr.

r-phantasus 1.30.0
Propagated dependencies: r-yaml@2.3.10 r-xml@3.99-0.20 r-tidyr@1.3.1 r-svglite@2.2.2 r-stringr@1.6.0 r-scales@1.4.0 r-rook@1.2 r-rhdf5client@1.32.0 r-rhdf5@2.54.0 r-protolite@2.3.1 r-pheatmap@1.0.13 r-phantasuslite@1.8.0 r-opencpu@2.2.14 r-matrix@1.7-4 r-limma@3.66.0 r-jsonlite@2.0.0 r-httr@1.4.7 r-httpuv@1.6.16 r-htmltools@0.5.8.1 r-gtable@0.3.6 r-ggplot2@4.0.1 r-geoquery@2.78.0 r-fs@1.6.6 r-fgsea@1.36.0 r-edger@4.8.0 r-deseq2@1.50.2 r-data-table@1.17.8 r-curl@7.0.0 r-config@0.3.2 r-ccapp@0.3.5 r-biobase@2.70.0 r-assertthat@0.2.1 r-apeglm@1.32.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://alserglab.wustl.edu/phantasus
Licenses: Expat
Synopsis: Visual and interactive gene expression analysis
Description:

Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.

r-pd-medgene-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.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-hg-u95a 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.u95a
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for The Manufacturer's Name HG_U95A
Description:

Platform Design Info for The Manufacturer's Name HG_U95A.

r-pd-drosgenome1 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.drosgenome1
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for The Manufacturer's Name DrosGenome1
Description:

Platform Design Info for The Manufacturer's Name DrosGenome1.

r-plyxp 1.4.3
Propagated dependencies: r-vctrs@0.6.5 r-tidyselect@1.2.1 r-tidyr@1.3.1 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-s7@0.2.1 r-s4vectors@0.48.0 r-rlang@1.1.6 r-purrr@1.2.0 r-pillar@1.11.1 r-glue@1.8.0 r-dplyr@1.1.4 r-cli@3.6.5
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/jtlandis/plyxp
Licenses: Expat
Synopsis: Data masks for SummarizedExperiment enabling dplyr-like manipulation
Description:

The package provides `rlang` data masks for the SummarizedExperiment class. The enables the evaluation of unquoted expression in different contexts of the SummarizedExperiment object with optional access to other contexts. The goal for `plyxp` is for evaluation to feel like a data.frame object without ever needing to unwind to a rectangular data.frame.

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
Synopsis: Platform Design Info for Affymetrix BovGene-1_1-st
Description:

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

r-pwmenrich-hsapiens-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.Hsapiens.background
Licenses: GPL 3
Synopsis: H. sapiens background for PWMEnrich
Description:

PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs.

r-panp 1.80.0
Propagated dependencies: r-biobase@2.70.0 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/panp
Licenses: GPL 2+
Synopsis: Presence-Absence Calls from Negative Strand Matching Probesets
Description:

This package provides a function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.

r-primeviewcdf 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/primeviewcdf
Licenses: LGPL 2.0+
Synopsis: primeviewcdf
Description:

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

r-pd-moex-1-0-st-v1 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.moex.1.0.st.v1
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for Affymetrix MoEx-1_0-st-v1
Description:

Platform Design Info for Affymetrix MoEx-1_0-st-v1.

r-porcineprobe 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/porcineprobe
Licenses: LGPL 2.0+
Synopsis: Probe sequence data for microarrays of type porcine
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 Porcine\_probe\_tab.

r-pd-ht-mg-430a 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.ht.mg.430a
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for The Manufacturer's Name HT_MG-430A
Description:

Platform Design Info for The Manufacturer's Name HT_MG-430A.

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
Synopsis: Platform Design Info for The Manufacturer's Name RAE230B
Description:

Platform Design Info for The Manufacturer's Name RAE230B.

r-pepxmltab 1.44.0
Propagated dependencies: r-xml@3.99-0.20
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pepXMLTab
Licenses: Artistic License 2.0
Synopsis: Parsing pepXML files and filter based on peptide FDR
Description:

Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR.

r-pd-2006-07-18-hg18-refseq-promoter 1.8.1
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.2006.07.18.hg18.refseq.promoter
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for NimbleGen 2006-07-18_hg18_refseq_promoter
Description:

Platform Design Info for NimbleGen 2006-07-18_hg18_refseq_promoter.

r-pagerank 1.20.0
Propagated dependencies: r-motifmatchr@1.32.0 r-igraph@2.2.1 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/hd2326/pageRank
Licenses: GPL 2
Synopsis: Temporal and Multiplex PageRank for Gene Regulatory Network Analysis
Description:

Implemented temporal PageRank analysis as defined by Rozenshtein and Gionis. Implemented multiplex PageRank as defined by Halu et al. Applied temporal and multiplex PageRank in gene regulatory network analysis.

r-prostatecancercamcap 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/prostateCancerCamcap
Licenses: Artistic License 2.0
Synopsis: Prostate Cancer Data
Description:

This package provides a Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset.

r-pd-cyrgene-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.cyrgene.1.1.st
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for Affymetrix CyRGene-1_1-st
Description:

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

r-peco 1.22.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-scater@1.38.0 r-genlasso@1.6.1 r-foreach@1.5.2 r-doparallel@1.0.17 r-conicfit@1.0.4 r-circular@0.5-2 r-assertthat@0.2.1
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/jhsiao999/peco
Licenses: GPL 3+
Synopsis: Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
Description:

Our approach provides a way to assign continuous cell cycle phase using scRNA-seq data, and consequently, allows to identify cyclic trend of gene expression levels along the cell cycle. This package provides method and training data, which includes scRNA-seq data collected from 6 individual cell lines of induced pluripotent stem cells (iPSCs), and also continuous cell cycle phase derived from FUCCI fluorescence imaging data.

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
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-philr 1.36.0
Propagated dependencies: r-tidyr@1.3.1 r-phangorn@2.12.1 r-ggtree@4.0.1 r-ggplot2@4.0.1 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/jsilve24/philr
Licenses: GPL 3
Synopsis: Phylogenetic partitioning based ILR transform for metagenomics data
Description:

PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.

r-plasmut 1.8.0
Propagated dependencies: r-tibble@3.3.0 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/plasmut
Licenses: Artistic License 2.0
Synopsis: Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic, or somatic
Description:

This package provides a Bayesian method for quantifying the liklihood that a given plasma mutation arises from clonal hematopoesis or the underlying tumor. It requires sequencing data of the mutation in plasma and white blood cells with the number of distinct and mutant reads in both tissues. We implement a Monte Carlo importance sampling method to assess the likelihood that a mutation arises from the tumor relative to non-tumor origin.

r-plotgardener 1.16.0
Propagated dependencies: r-withr@3.0.2 r-strawr@0.0.92 r-rlang@1.1.6 r-rhdf5@2.54.0 r-rcpp@1.1.0 r-rcolorbrewer@1.1-3 r-purrr@1.2.0 r-plyranges@1.30.1 r-iranges@2.44.0 r-glue@1.8.0 r-ggplotify@0.1.3 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-dplyr@1.1.4 r-data-table@1.17.8 r-curl@7.0.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://phanstiellab.github.io/plotgardener
Licenses: Expat
Synopsis: Coordinate-Based Genomic Visualization Package for R
Description:

Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.

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Total results: 68249