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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-multiwgcna 1.7.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/multiWGCNA
Licenses: GPL 3
Build system: r
Synopsis: multiWGCNA
Description:

An R package for deeping mining gene co-expression networks in multi-trait expression data. Provides functions for analyzing, comparing, and visualizing WGCNA networks across conditions. multiWGCNA was designed to handle the common case where there are multiple biologically meaningful sample traits, such as disease vs wildtype across development or anatomical region.

r-mirit 1.6.2
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/jacopo-ronchi/MIRit
Licenses: GPL 3+
Build system: r
Synopsis: Integrate microRNA and gene expression to decipher pathway complexity
Description:

MIRit is an R package that provides several methods for investigating the relationships between miRNAs and genes in different biological conditions. In particular, MIRit allows to explore the functions of dysregulated miRNAs, and makes it possible to identify miRNA-gene regulatory axes that control biological pathways, thus enabling the users to unveil the complexity of miRNA biology. MIRit is an all-in-one framework that aims to help researchers in all the central aspects of an integrative miRNA-mRNA analyses, from differential expression analysis to network characterization.

r-mpedbarray-db 3.2.3
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/mpedbarray.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: FHCRC Nelson Lab mpedbarray Annotation Data (mpedbarray)
Description:

FHCRC Nelson Lab mpedbarray Annotation Data (mpedbarray) assembled using data from public repositories.

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-mafdb-topmed-freeze5-hg38 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.TOPMed.freeze5.hg38
Licenses: Artistic License 2.0
Build system: r
Synopsis: Minor allele frequency data from TOPMed for hg38
Description:

Store minor allele frequency data from NHLBI TOPMed for the human genome version hg38.

r-mousefm 1.20.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MouseFM
Licenses: GPL 3
Build system: r
Synopsis: In-silico methods for genetic finemapping in inbred mice
Description:

This package provides methods for genetic finemapping in inbred mice by taking advantage of their very high homozygosity rate (>95%).

r-methylseqdata 1.20.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-rhdf5@2.54.0 r-iranges@2.44.0 r-hdf5array@1.38.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MethylSeqData
Licenses: CC0
Build system: r
Synopsis: Collection of Public DNA Methylation Sequencing Datasets
Description:

Base-level (i.e. cytosine-level) counts for a collection of public bisulfite-seq datasets (e.g., WGBS and RRBS), provided as SummarizedExperiment objects with sample- and base-level metadata.

r-mu11ksubb-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/mu11ksubb.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix Mu11KsubB Array annotation data (chip mu11ksubb)
Description:

Affymetrix Affymetrix Mu11KsubB Array annotation data (chip mu11ksubb) assembled using data from public repositories.

r-maizeprobe 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/maizeprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type maize
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 Maize\_probe\_tab.

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.

r-moexexonprobesetlocation 1.15.0
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/MoExExonProbesetLocation
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type MoEx
Description:

This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible.

r-mariner 1.10.2
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-mirbaseversions-db 1.1.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/miRBaseVersions.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Collection of mature miRNA names of 22 different miRBase release versions
Description:

Annotation package containing all available miRNA names from 22 versions (data from http://www.mirbase.org/).

r-moe430b-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/moe430b.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix MOE430B Array annotation data (chip moe430b)
Description:

Affymetrix Affymetrix MOE430B Array annotation data (chip moe430b) assembled using data from public repositories.

r-mist 1.2.3
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.

r-motifpeeker 1.2.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/neurogenomics/MotifPeeker
Licenses: GPL 3+
Build system: r
Synopsis: Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
Description:

MotifPeeker is used to compare and analyse datasets from epigenomic profiling methods with motif enrichment as the key benchmark. The package outputs an HTML report consisting of three sections: (1. General Metrics) Overview of peaks-related general metrics for the datasets (FRiP scores, peak widths and motif-summit distances). (2. Known Motif Enrichment Analysis) Statistics for the frequency of user-provided motifs enriched in the datasets. (3. De-Novo Motif Enrichment Analysis) Statistics for the frequency of de-novo discovered motifs enriched in the datasets and compared with known motifs.

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
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-moda 1.36.0
Propagated dependencies: r-wgcna@1.73 r-rcolorbrewer@1.1-3 r-igraph@2.2.1 r-dynamictreecut@1.63-1 r-cluster@2.1.8.1 r-amountain@1.36.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MODA
Licenses: GPL 2+
Build system: r
Synopsis: MODA: MOdule Differential Analysis for weighted gene co-expression network
Description:

MODA can be used to estimate and construct condition-specific gene co-expression networks, and identify differentially expressed subnetworks as conserved or condition specific modules which are potentially associated with relevant biological processes.

r-microbiomeexplorer 1.20.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/microbiomeExplorer
Licenses: Expat
Build system: r
Synopsis: Microbiome Exploration App
Description:

The MicrobiomeExplorer R package is designed to facilitate the analysis and visualization of marker-gene survey feature data. It allows a user to perform and visualize typical microbiome analytical workflows either through the command line or an interactive Shiny application included with the package. In addition to applying common analytical workflows the application enables automated analysis report generation.

r-mafdb-exac-r1-0-nontcga-grch38 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.GRCh38
Licenses: Artistic License 2.0
Build system: r
Synopsis: Minor allele frequency data from ExAC release 1.0 subset of nonTCGA exomes for GRCh38
Description:

Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0 subset of nonTCGA exomes) for the human genome version GRCh38.

r-multirnaflow 1.8.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/loubator/MultiRNAflow
Licenses: GPL 3 FSDG-compatible
Build system: r
Synopsis: An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions
Description:

Our R package MultiRNAflow provides an easy to use unified framework allowing to automatically make both unsupervised and supervised (DE) analysis for datasets with an arbitrary number of biological conditions and time points. In particular, our code makes a deep downstream analysis of DE information, e.g. identifying temporal patterns across biological conditions and DE genes which are specific to a biological condition for each time.

r-mineica 1.49.0
Propagated dependencies: r-xtable@1.8-4 r-scales@1.4.0 r-rgraphviz@2.54.0 r-rcolorbrewer@1.1-3 r-plyr@1.8.9 r-mclust@6.1.2 r-marray@1.88.0 r-lumihumanall-db@1.22.0 r-lumi@2.62.0 r-jade@2.0-4 r-igraph@2.2.1 r-hmisc@5.2-4 r-gtools@3.9.5 r-graph@1.88.0 r-gostats@2.76.0 r-ggplot2@4.0.1 r-fpc@2.2-13 r-foreach@1.5.2 r-fastica@1.2-7 r-colorspace@2.1-2 r-cluster@2.1.8.1 r-biomart@2.66.0 r-biocgenerics@0.56.0 r-biobase@2.70.0 r-annotationdbi@1.72.0 r-annotate@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MineICA
Licenses: GPL 2
Build system: r
Synopsis: Analysis of an ICA decomposition obtained on genomics data
Description:

The goal of MineICA is to perform Independent Component Analysis (ICA) on multiple transcriptome datasets, integrating additional data (e.g molecular, clinical and pathological). This Integrative ICA helps the biological interpretation of the components by studying their association with variables (e.g sample annotations) and gene sets, and enables the comparison of components from different datasets using correlation-based graph.

r-msa2dist 1.14.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://gitlab.gwdg.de/mpievolbio-it/MSA2dist
Licenses: FSDG-compatible
Build system: r
Synopsis: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis
Description:

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calculations which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances. DNAStringSet alignments can be analysed as codon alignments to look for synonymous and nonsynonymous substitutions (dN/dS) in a parallelised fashion using a variety of substitution models. Non-aligned coding sequences can be directly used to construct pairwise codon alignments (global/local) and calculate dN/dS without any external dependencies.

r-msstatsqc 2.28.0
Propagated dependencies: r-qcmetrics@1.48.0 r-plotly@4.11.0 r-msnbase@2.36.0 r-ggplot2@4.0.1 r-ggextra@0.11.0 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://msstats.org/msstatsqc
Licenses: FSDG-compatible
Build system: r
Synopsis: Longitudinal system suitability monitoring and quality control for proteomic experiments
Description:

MSstatsQC is an R package which provides longitudinal system suitability monitoring and quality control tools for proteomic experiments.

Total results: 2911