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

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-mouse-db0 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mouse.db0
Licenses: Artistic License 2.0
Build system: r
Synopsis: Base Level Annotation databases for mouse
Description:

Base annotation databases for mouse, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

r-miadash 1.2.0
Propagated dependencies: r-vegan@2.7-2 r-treesummarizedexperiment@2.18.0 r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-shinywidgets@0.9.0 r-shinyjs@2.1.0 r-shinydashboard@0.7.3 r-shiny@1.11.1 r-scuttle@1.20.0 r-scater@1.38.0 r-s4vectors@0.48.0 r-rintrojs@0.3.4 r-mia@1.18.0 r-iseetree@1.4.0 r-isee@2.22.0 r-htmltools@0.5.8.1 r-bluster@1.20.0 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/microbiome/miaDash
Licenses: Artistic License 2.0
Build system: r
Synopsis: Dashboard for the interactive analysis and exploration of microbiome data
Description:

miaDash provides a Graphical User Interface for the exploration of microbiome data. This way, no knowledge of programming is required to perform analyses. Datasets can be imported, manipulated, analysed and visualised with a user-friendly interface.

r-mirna102xgaincdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mirna102xgaincdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: mirna102xgaincdf
Description:

This package provides a package containing an environment representing the miRNA-1_0_2Xgain.CDF file.

r-mmdiffbamsubset 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MMDiffBamSubset
Licenses: LGPL 2.0+
Build system: r
Synopsis: Example ChIP-Seq data for the MMDiff package
Description:

Subset of BAM files, including WT_2.bam, Null_2.bam, Resc_2.bam, Input.bam from the "Cfp1" experiment (see Clouaire et al., Genes Dev. 2012). Data is available under ArrayExpress accession numbers E-ERAD-79. Additionally, corresponding subset of peaks called by MACS.

r-mgu74bv2-db 3.13.0
Propagated dependencies: r-org-mm-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mgu74bv2.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix MG_U74Bv2 Array annotation data (chip mgu74bv2)
Description:

Affymetrix Affymetrix MG_U74Bv2 Array annotation data (chip mgu74bv2) assembled using data from public repositories.

r-mouse4302probe 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mouse4302probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type mouse4302
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 Mouse430\_2\_probe\_tab.

r-mirnapath 1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/miRNApath
Licenses: LGPL 2.1
Build system: r
Synopsis: miRNApath: Pathway Enrichment for miRNA Expression Data
Description:

This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes.

r-midashla 1.18.0
Propagated dependencies: r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringi@1.8.7 r-s4vectors@0.48.0 r-rlang@1.1.6 r-qdaptools@1.3.7 r-multiassayexperiment@1.36.1 r-magrittr@2.0.4 r-knitr@1.50 r-kableextra@1.4.0 r-hardyweinberg@1.7.9 r-formattable@0.2.1 r-dplyr@1.1.4 r-broom@1.0.10 r-assertthat@0.2.1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/midasHLA
Licenses: FSDG-compatible
Build system: r
Synopsis: R package for immunogenomics data handling and association analysis
Description:

MiDAS is a R package for immunogenetics data transformation and statistical analysis. MiDAS accepts input data in the form of HLA alleles and KIR types, and can transform it into biologically meaningful variables, enabling HLA amino acid fine mapping, analyses of HLA evolutionary divergence, KIR gene presence, as well as validated HLA-KIR interactions. Further, it allows comprehensive statistical association analysis workflows with phenotypes of diverse measurement scales. MiDAS closes a gap between the inference of immunogenetic variation and its efficient utilization to make relevant discoveries related to T cell, Natural Killer cell, and disease biology.

r-mafdb-exac-r1-0-hs37d5 3.10.0
Propagated dependencies: r-s4vectors@0.48.0 r-iranges@2.44.0 r-genomicscores@2.22.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MafDb.ExAC.r1.0.hs37d5
Licenses: Artistic License 2.0
Build system: r
Synopsis: Minor allele frequency data from ExAC release 1.0 for hs37d5
Description:

Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0) for the human genome version hs37d5.

r-mirintegrator 1.40.0
Propagated dependencies: r-rontotools@2.38.0 r-rgraphviz@2.54.0 r-org-hs-eg-db@3.22.0 r-graph@1.88.0 r-ggplot2@4.0.1 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://datad.github.io/mirIntegrator/
Licenses: GPL 3+
Build system: r
Synopsis: Integrating microRNA expression into signaling pathways for pathway analysis
Description:

This package provides tools for augmenting signaling pathways to perform pathway analysis of microRNA and mRNA expression levels.

r-mu19ksubbcdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mu19ksubbcdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: mu19ksubbcdf
Description:

This package provides a package containing an environment representing the Mu19KsubB.CDF file.

r-mgu74acdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mgu74acdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: mgu74acdf
Description:

This package provides a package containing an environment representing the MG_U74A.cdf file.

r-multistateqtl 2.2.0
Propagated dependencies: r-viridis@0.6.5 r-tidyr@1.3.1 r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-qtlexperiment@2.2.0 r-matrixstats@1.5.0 r-mashr@0.2.79 r-ggplot2@4.0.1 r-fitdistrplus@1.2-4 r-dplyr@1.1.4 r-data-table@1.17.8 r-complexheatmap@2.26.0 r-collapse@2.1.5 r-circlize@0.4.16
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/dunstone-a/multistateQTL
Licenses: GPL 3
Build system: r
Synopsis: Toolkit for the analysis of multi-state QTL data
Description:

This package provides a collection of tools for doing various analyses of multi-state QTL data, with a focus on visualization and interpretation. The package multistateQTL contains functions which can remove or impute missing data, identify significant associations, as well as categorise features into global, multi-state or unique. The analysis results are stored in a QTLExperiment object, which is based on the SummarisedExperiment framework.

r-methylimp2 1.6.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-corpcor@1.6.10 r-champdata@2.42.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/annaplaksienko/methyLImp2
Licenses: GPL 3
Build system: r
Synopsis: Missing value estimation of DNA methylation data
Description:

This package allows to estimate missing values in DNA methylation data. methyLImp method is based on linear regression since methylation levels show a high degree of inter-sample correlation. Implementation is parallelised over chromosomes since probes on different chromosomes are usually independent. Mini-batch approach to reduce the runtime in case of large number of samples is available.

r-mu11ksubbprobe 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mu11ksubbprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type mu11ksubb
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 Mu11KsubB\_probe\_tab.

r-mogene21sttranscriptcluster-db 8.8.0
Propagated dependencies: r-org-mm-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mogene21sttranscriptcluster.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix mogene21 annotation data (chip mogene21sttranscriptcluster)
Description:

Affymetrix mogene21 annotation data (chip mogene21sttranscriptcluster) assembled using data from public repositories.

r-mariner 1.10.2
Propagated dependencies: r-summarizedexperiment@1.40.0 r-strawr@0.0.92 r-s4vectors@0.48.0 r-rlang@1.1.6 r-rhdf5@2.54.0 r-rcolorbrewer@1.1-3 r-purrr@1.2.0 r-progress@1.2.3 r-plotgardener@1.16.0 r-magrittr@2.0.4 r-iranges@2.44.0 r-interactionset@1.38.0 r-hdf5array@1.38.0 r-glue@1.8.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-dplyr@1.1.4 r-delayedarray@0.36.0 r-dbscan@1.2.3 r-data-table@1.17.8 r-colourvalues@0.3.11 r-biocparallel@1.44.0 r-biocmanager@1.30.27 r-biocgenerics@0.56.0 r-assertthat@0.2.1 r-abind@1.4-8
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://ericscottdavis.com/mariner/
Licenses: Expat
Build system: r
Synopsis: Mariner: Explore the Hi-Cs
Description:

This package provides tools for manipulating paired ranges and working with Hi-C data in R. Functionality includes manipulating/merging paired regions, generating paired ranges, extracting/aggregating interactions from `.hic` files, and visualizing the results. Designed for compatibility with plotgardener for visualization.

r-mirnatap-db 0.99.10
Propagated dependencies: r-rsqlite@2.4.4 r-mirnatap@1.44.0 r-dbi@1.2.3 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/miRNAtap.db
Licenses: GPL 2
Build system: r
Synopsis: Data for miRNAtap
Description:

This package holds the database for miRNAtap.

r-mouse430a2cdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mouse430a2cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: mouse430a2cdf
Description:

This package provides a package containing an environment representing the Mouse430A_2.cdf file.

r-mouse430a2probe 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mouse430a2probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type mouse430a2
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 Mouse430A\_2\_probe\_tab.

r-mafdb-exac-r1-0-nontcga-hs37d5 3.10.0
Propagated dependencies: r-s4vectors@0.48.0 r-iranges@2.44.0 r-genomicscores@2.22.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MafDb.ExAC.r1.0.nonTCGA.hs37d5
Licenses: Artistic License 2.0
Build system: r
Synopsis: Minor allele frequency data from ExAC release 1.0 subset of nonTCGA exomes for hs37d5
Description:

Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0 subset of nonTCGA exomes) for the human genome version hs37d5.

r-mspurity 1.36.0
Propagated dependencies: r-stringr@1.6.0 r-rsqlite@2.4.4 r-reshape2@1.4.5 r-rcpp@1.1.0 r-plyr@1.8.9 r-mzr@2.44.0 r-magrittr@2.0.4 r-ggplot2@4.0.1 r-foreach@1.5.2 r-fastcluster@1.3.0 r-dplyr@1.1.4 r-dosnow@1.0.20 r-dbplyr@2.5.1 r-dbi@1.2.3
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/computational-metabolomics/msPurity/
Licenses: FSDG-compatible
Build system: r
Synopsis: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Description:

msPurity R package was developed to: 1) Assess the spectral quality of fragmentation spectra by evaluating the "precursor ion purity". 2) Process fragmentation spectra. 3) Perform spectral matching. What is precursor ion purity? -What we call "Precursor ion purity" is a measure of the contribution of a selected precursor peak in an isolation window used for fragmentation. The simple calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window. When assessing MS/MS spectra this calculation is done before and after the MS/MS scan of interest and the purity is interpolated at the recorded time of the MS/MS acquisition. Additionally, isotopic peaks can be removed, low abundance peaks are removed that are thought to have limited contribution to the resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used to normalise the intensities used for the calculation.

r-mofa2 1.20.2
Dependencies: python-scikit-learn@1.7.0 python-scipy@1.12.0 python@3.11.14 python-pandas@2.2.3 python-numpy@1.26.4 python-h5py@3.13.0 argparse@1.1.0
Propagated dependencies: r-uwot@0.2.4 r-tidyr@1.3.1 r-stringi@1.8.7 r-rtsne@0.17 r-rhdf5@2.54.0 r-reticulate@1.44.1 r-reshape2@1.4.5 r-rcolorbrewer@1.1-3 r-pheatmap@1.0.13 r-magrittr@2.0.4 r-hdf5array@1.38.0 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-forcats@1.0.1 r-dplyr@1.1.4 r-delayedarray@0.36.0 r-cowplot@1.2.0 r-corrplot@0.95 r-basilisk@1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://biofam.github.io/MOFA2/index.html
Licenses: FSDG-compatible
Build system: r
Synopsis: Multi-Omics Factor Analysis v2
Description:

The MOFA2 package contains a collection of tools for training and analysing multi-omic factor analysis (MOFA). MOFA is a probabilistic factor model that aims to identify principal axes of variation from data sets that can comprise multiple omic layers and/or groups of samples. Additional time or space information on the samples can be incorporated using the MEFISTO framework, which is part of MOFA2. Downstream analysis functions to inspect molecular features underlying each factor, vizualisation, imputation etc are available.

r-mist 1.2.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rlang@1.1.6 r-mvtnorm@1.3-3 r-mcmcpack@1.7-1 r-matrix@1.7-4 r-car@3.1-3 r-biocparallel@1.44.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://https://github.com/dxd429/mist
Licenses: Expat
Build system: r
Synopsis: Differential Methylation Analysis for scDNAm Data
Description:

mist (Methylation Inference for Single-cell along Trajectory) is a hierarchical Bayesian framework for modeling DNA methylation trajectories and performing differential methylation (DM) analysis in single-cell DNA methylation (scDNAm) data. It estimates developmental-stage-specific variations, identifies genomic features with drastic changes along pseudotime, and, for two phenotypic groups, detects features with distinct temporal methylation patterns. mist uses Gibbs sampling to estimate parameters for temporal changes and stage-specific variations.

Total results: 2909