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      /\__ \     / /\ \ \\ \ \_/ / /     / / /\ \__
     / /_ \ \   / / /\ \ \\ \___/ /     / / /\ \___\
    / / /\ \ \ / / /  \ \_\\ \ \_/      \ \ \ \/___/
   / / /  \/_// / /   / / / \ \ \        \ \ \
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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-msstatsbionet 1.2.0
Propagated dependencies: r-tidyr@1.3.1 r-rcy3@2.30.0 r-r2r@0.1.2 r-msstats@4.18.1 r-jsonlite@2.0.0 r-httr@1.4.7
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://msstats.org
Licenses: FSDG-compatible
Build system: r
Synopsis: Network Analysis for MS-based Proteomics Experiments
Description:

This package provides a set of tools for network analysis using mass spectrometry-based proteomics data and network databases. The package takes as input the output of MSstats differential abundance analysis and provides functions to perform enrichment analysis and visualization in the context of prior knowledge from past literature. Notably, this package integrates with INDRA, which is a database of biological networks extracted from the literature using text mining techniques.

r-metahdep 1.68.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/metahdep
Licenses: GPL 3
Build system: r
Synopsis: Hierarchical Dependence in Meta-Analysis
Description:

This package provides tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies.

r-multiwgcnadata 1.8.0
Propagated dependencies: r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/multiWGCNAdata
Licenses: Artistic License 2.0
Build system: r
Synopsis: Data Package for multiWGCNA
Description:

Stores expression profiling data from experiments compatible with the multiWGCNA R package. This includes human postmortem microarray data from patients and controls (GSE28521), astrocyte Ribotag RNA-seq data from EAE and wildtype mice (GSE100329), and mouse RNA-seq data from tau pathology (rTg4510) and wildtype control mice (GSE125957). These data can be accessed using the ExperimentHub workflow (see multiWGCNA vignettes).

r-metagene2 1.26.0
Propagated dependencies: r-rtracklayer@1.70.0 r-rsamtools@2.26.0 r-reshape2@1.4.5 r-r6@2.6.1 r-purrr@1.2.0 r-magrittr@2.0.4 r-iranges@2.44.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicalignments@1.46.0 r-genomeinfodb@1.46.0 r-dplyr@1.1.4 r-data-table@1.17.8 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/ArnaudDroitLab/metagene2
Licenses: Artistic License 2.0
Build system: r
Synopsis: package to produce metagene plots
Description:

This package produces metagene plots to compare coverages of sequencing experiments at selected groups of genomic regions. It can be used for such analyses as assessing the binding of DNA-interacting proteins at promoter regions or surveying antisense transcription over the length of a gene. The metagene2 package can manage all aspects of the analysis, from normalization of coverages to plot facetting according to experimental metadata. Bootstraping analysis is used to provide confidence intervals of per-sample mean coverages.

r-mimager 1.34.0
Propagated dependencies: r-scales@1.4.0 r-s4vectors@0.48.0 r-preprocesscore@1.72.0 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-gtable@0.3.6 r-dbi@1.2.3 r-biocgenerics@0.56.0 r-biobase@2.70.0 r-affyplm@1.86.0 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/aaronwolen/mimager
Licenses: Expat
Build system: r
Synopsis: mimager: The Microarray Imager
Description:

Easily visualize and inspect microarrays for spatial artifacts.

r-mygene 1.46.0
Propagated dependencies: r-txdbmaker@1.6.0 r-sqldf@0.4-11 r-s4vectors@0.48.0 r-plyr@1.8.9 r-jsonlite@2.0.0 r-httr@1.4.7 r-hmisc@5.2-4 r-genomicfeatures@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mygene
Licenses: Artistic License 2.0
Build system: r
Synopsis: Access MyGene.Info_ services
Description:

MyGene.Info_ provides simple-to-use REST web services to query/retrieve gene annotation data. It's designed with simplicity and performance emphasized. *mygene*, is an easy-to-use R wrapper to access MyGene.Info_ services.

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-mgnifyr 1.6.1
Propagated dependencies: r-urltools@1.7.3.1 r-treesummarizedexperiment@2.18.0 r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-reshape2@1.4.5 r-plyr@1.8.9 r-multiassayexperiment@1.36.1 r-mia@1.18.0 r-httr@1.4.7 r-dplyr@1.1.4 r-biocgenerics@0.56.0 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/EBI-Metagenomics/MGnifyR
Licenses: Artistic License 2.0 FSDG-compatible
Build system: r
Synopsis: R interface to EBI MGnify metagenomics resource
Description:

Utility package to facilitate integration and analysis of EBI MGnify data in R. The package can be used to import microbial data for instance into TreeSummarizedExperiment (TreeSE). In TreeSE format, the data is directly compatible with miaverse framework.

r-moe430bprobe 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/moe430bprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type moe430b
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 MOE430B\_probe\_tab.

r-mapfx 1.6.3
Propagated dependencies: r-xgboost@1.7.11.1 r-uwot@0.2.4 r-stringr@1.6.0 r-rfast@2.1.5.2 r-reshape2@1.4.5 r-rcolorbrewer@1.1-3 r-pbapply@1.7-4 r-igraph@2.2.1 r-icellr@1.7.0 r-gtools@3.9.5 r-glmnetutils@1.1.9 r-ggplot2@4.0.1 r-flowcore@2.22.0 r-e1071@1.7-16 r-cowplot@1.2.0 r-complexheatmap@2.26.0 r-circlize@0.4.16 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/HsiaoChiLiao/MAPFX
Licenses: GPL 2
Build system: r
Synopsis: MAssively Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry Experiments
Description:

MAPFX is an end-to-end toolbox that pre-processes the raw data from MPC experiments (e.g., BioLegend's LEGENDScreen and BD Lyoplates assays), and further imputes the ‘missing’ infinity markers in the wells without those measurements. The pipeline starts by performing background correction on raw intensities to remove the noise from electronic baseline restoration and fluorescence compensation by adapting a normal-exponential convolution model. Unwanted technical variation, from sources such as well effects, is then removed using a log-normal model with plate, column, and row factors, after which infinity markers are imputed using the informative backbone markers as predictors. The completed dataset can then be used for clustering and other statistical analyses. Additionally, MAPFX can be used to normalise data from FFC assays as well.

r-mgu74av2cdf 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/mgu74av2cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: mgu74av2cdf
Description:

This package provides a package containing an environment representing the MG_U74Av2.CDF file.

r-mutscan 1.0.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-xfun@0.54 r-tidyselect@1.2.1 r-tidyr@1.3.1 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-rmarkdown@2.30 r-rlang@1.1.6 r-rcpp@1.1.0 r-matrix@1.7-4 r-limma@3.66.0 r-iranges@2.44.0 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-ggally@2.4.0 r-edger@4.8.0 r-dt@0.34.0 r-dplyr@1.1.4 r-delayedarray@0.36.0 r-csaw@1.44.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/fmicompbio/mutscan
Licenses: Expat
Build system: r
Synopsis: Preprocessing and Analysis of Deep Mutational Scanning Data
Description:

This package provides functionality for processing and statistical analysis of multiplexed assays of variant effect (MAVE) and similar data. The package contains functions covering the full workflow from raw FASTQ files to publication-ready visualizations. A broad range of library designs can be processed with a single, unified interface.

r-mofadata 1.26.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MOFAdata
Licenses: LGPL 3
Build system: r
Synopsis: Data package for Multi-Omics Factor Analysis (MOFA)
Description:

This package provides a collection of datasets to accompany the R package MOFA and illustrate running and analysing MOFA models.

r-mspuritydata 1.38.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/msPurityData
Licenses: GPL 2+
Build system: r
Synopsis: Fragmentation spectral libraries and data to test the msPurity package
Description:

Fragmentation spectral libraries and data to test the msPurity package.

r-mapscape 1.34.0
Propagated dependencies: r-stringr@1.6.0 r-jsonlite@2.0.0 r-htmlwidgets@1.6.4 r-base64enc@0.1-3
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mapscape
Licenses: GPL 3
Build system: r
Synopsis: mapscape
Description:

MapScape integrates clonal prevalence, clonal hierarchy, anatomic and mutational information to provide interactive visualization of spatial clonal evolution. There are four inputs to MapScape: (i) the clonal phylogeny, (ii) clonal prevalences, (iii) an image reference, which may be a medical image or drawing and (iv) pixel locations for each sample on the referenced image. Optionally, MapScape can accept a data table of mutations for each clone and their variant allele frequencies in each sample. The output of MapScape consists of a cropped anatomical image surrounded by two representations of each tumour sample. The first, a cellular aggregate, visually displays the prevalence of each clone. The second shows a skeleton of the clonal phylogeny while highlighting only those clones present in the sample. Together, these representations enable the analyst to visualize the distribution of clones throughout anatomic space.

r-mu11ksubbcdf 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/mu11ksubbcdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: mu11ksubbcdf
Description:

This package provides a package containing an environment representing the Mu11KsubB.CDF file.

r-mosbi 1.16.0
Propagated dependencies: r-xml2@1.5.0 r-rcppparallel@5.1.11-1 r-rcpp@1.1.0 r-rcolorbrewer@1.1-3 r-qubic@1.38.0 r-isa2@0.3.6 r-igraph@2.2.1 r-fabia@2.56.0 r-biclust@2.0.3.1 r-bh@1.87.0-1 r-akmbiclust@0.1.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mosbi
Licenses: FSDG-compatible
Build system: r
Synopsis: Molecular Signature identification using Biclustering
Description:

This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics data. This is done by computing similarity networks of biclusters and filtering for overlaps using a custom error model. After that, the louvain modularity it used to extract bicluster communities from the similarity network, which can then be converted to ensemble biclusters. Additionally, MoSBi includes several network visualization methods to give an intuitive and scalable overview of the results. MoSBi comes with several biclustering algorithms, but can be easily extended to new biclustering algorithms.

r-mspms 1.2.0
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-rstatix@0.7.3 r-rlang@1.1.6 r-readr@2.1.6 r-qfeatures@1.20.0 r-purrr@1.2.0 r-magrittr@2.0.4 r-limma@3.66.0 r-heatmaply@1.6.0 r-ggseqlogo@0.2 r-ggpubr@0.6.2 r-ggplot2@4.0.1 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/baynec2/mspms
Licenses: Expat
Build system: r
Synopsis: Tools for the analysis of MSP-MS data
Description:

This package provides functions for the analysis of data generated by the multiplex substrate profiling by mass spectrometry for proteases (MSP-MS) method. Data exported from upstream proteomics software is accepted as input and subsequently processed for analysis. Tools for statistical analysis, visualization, and interpretation of the data are provided.

r-matter 2.12.0
Propagated dependencies: r-protgenerics@1.42.0 r-matrix@1.7-4 r-irlba@2.3.5.1 r-digest@0.6.39 r-biocparallel@1.44.0 r-biocgenerics@0.56.0 r-bh@1.87.0-1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/kuwisdelu/matter
Licenses: Artistic License 2.0 FSDG-compatible
Build system: r
Synopsis: Out-of-core statistical computing and signal processing
Description:

Toolbox for larger-than-memory scientific computing and visualization, providing efficient out-of-core data structures using files or shared memory, for dense and sparse vectors, matrices, and arrays, with applications to nonuniformly sampled signals and images.

r-msimpute 1.20.0
Dependencies: python@3.11.14
Propagated dependencies: r-tidyr@1.3.1 r-softimpute@1.4-3 r-scran@1.38.0 r-reticulate@1.44.1 r-pdist@1.2.1 r-mvtnorm@1.3-3 r-matrixstats@1.5.0 r-limma@3.66.0 r-fnn@1.1.4.1 r-dplyr@1.1.4 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/msImpute
Licenses: FSDG-compatible
Build system: r
Synopsis: Imputation of label-free mass spectrometry peptides
Description:

MsImpute is a package for imputation of peptide intensity in proteomics experiments. It additionally contains tools for MAR/MNAR diagnosis and assessment of distortions to the probability distribution of the data post imputation. The missing values are imputed by low-rank approximation of the underlying data matrix if they are MAR (method = "v2"), by Barycenter approach if missingness is MNAR ("v2-mnar"), or by Peptide Identity Propagation (PIP).

r-mosim 2.6.0
Propagated dependencies: r-zoo@1.8-14 r-stringr@1.6.0 r-stringi@1.8.7 r-signac@1.12.0-1.8ecdde2 r-seurat@5.3.1 r-scran@1.38.0 r-s4vectors@0.48.0 r-rlang@1.1.6 r-rcpp@1.1.0 r-matrixstats@1.5.0 r-lazyeval@0.2.2 r-iranges@2.44.0 r-hiddenmarkov@1.8-14 r-ggplot2@4.0.1 r-edger@4.8.0 r-dplyr@1.1.4 r-cpp11@0.5.2
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/ConesaLab/MOSim
Licenses: GPL 3
Build system: r
Synopsis: Multi-Omics Simulation (MOSim)
Description:

MOSim package simulates multi-omic experiments that mimic regulatory mechanisms within the cell, allowing flexible experimental design including time course and multiple groups.

r-mu19ksubb-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/mu19ksubb.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix Mu19KsubB Array annotation data (chip mu19ksubb)
Description:

Affymetrix Affymetrix Mu19KsubB Array annotation data (chip mu19ksubb) assembled using data from public repositories.

r-mipp 1.82.0
Propagated dependencies: r-mass@7.3-65 r-e1071@1.7-16 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/
Licenses: GPL 2+
Build system: r
Synopsis: Misclassification Penalized Posterior Classification
Description:

This package finds optimal sets of genes that seperate samples into two or more classes.

r-metabomxtr 1.44.0
Propagated dependencies: r-plyr@1.8.9 r-optimx@2025-4.9 r-multtest@2.66.0 r-ggplot2@4.0.1 r-formula@1.2-5 r-biocparallel@1.44.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/metabomxtr
Licenses: GPL 2
Build system: r
Synopsis: package to run mixture models for truncated metabolomics data with normal or lognormal distributions
Description:

The functions in this package return optimized parameter estimates and log likelihoods for mixture models of truncated data with normal or lognormal distributions.

Total results: 2909