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

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-mouse430a2-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/mouse430a2.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix Mouse430A_2 Array annotation data (chip mouse430a2)
Description:

Affymetrix Affymetrix Mouse430A_2 Array annotation data (chip mouse430a2) assembled using data from public repositories.

r-mgu74b-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/mgu74b.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix MG_U74B Array annotation data (chip mgu74b)
Description:

Affymetrix Affymetrix MG_U74B Array annotation data (chip mgu74b) 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-mgu74bv2probe 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/mgu74bv2probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type mgu74bv2
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 MG-U74Bv2\_probe\_tab.

r-msstatsbig 1.8.1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MSstatsBig
Licenses: Artistic License 2.0
Build system: r
Synopsis: MSstats Preprocessing for Larger than Memory Data
Description:

MSstats package provide tools for preprocessing, summarization and differential analysis of mass spectrometry (MS) proteomics data. Recently, some MS protocols enable acquisition of data sets that result in larger than memory quantitative data. MSstats functions are not able to process such data. MSstatsBig package provides additional converter functions that enable processing larger than memory data sets.

r-microbiomeprofiler 1.16.0
Propagated dependencies: r-yulab-utils@0.2.1 r-shinywidgets@0.9.0 r-shinycustomloader@0.9.0 r-shiny@1.11.1 r-magrittr@2.0.4 r-htmltools@0.5.8.1 r-gson@0.1.0 r-golem@0.5.1 r-ggplot2@4.0.1 r-enrichplot@1.30.3 r-dt@0.34.0 r-config@0.3.2 r-clusterprofiler@4.18.2
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/YuLab-SMU/MicrobiomeProfiler/
Licenses: GPL 2
Build system: r
Synopsis: An R/shiny package for microbiome functional enrichment analysis
Description:

This is an R/shiny package to perform functional enrichment analysis for microbiome data. This package was based on clusterProfiler. Moreover, MicrobiomeProfiler support KEGG enrichment analysis, COG enrichment analysis, Microbe-Disease association enrichment analysis, Metabo-Pathway analysis.

r-methtargetedngs 1.42.0
Dependencies: hmmer@3.3.2
Propagated dependencies: r-stringr@1.6.0 r-seqinr@4.2-36 r-pwalign@1.6.0 r-gplots@3.2.0 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MethTargetedNGS
Licenses: Artistic License 2.0
Build system: r
Synopsis: Perform Methylation Analysis on Next Generation Sequencing Data
Description:

Perform step by step methylation analysis of Next Generation Sequencing data.

r-mpranalyze 1.28.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-progress@1.2.3 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/YosefLab/MPRAnalyze
Licenses: GPL 3
Build system: r
Synopsis: Statistical Analysis of MPRA data
Description:

MPRAnalyze provides statistical framework for the analysis of data generated by Massively Parallel Reporter Assays (MPRAs), used to directly measure enhancer activity. MPRAnalyze can be used for quantification of enhancer activity, classification of active enhancers and comparative analyses of enhancer activity between conditions. MPRAnalyze construct a nested pair of generalized linear models (GLMs) to relate the DNA and RNA observations, easily adjustable to various experimental designs and conditions, and provides a set of rigorous statistical testig schemes.

r-modcon 1.18.0
Dependencies: perl@5.36.0
Propagated dependencies: r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/caggtaagtat/ModCon
Licenses: FSDG-compatible
Build system: r
Synopsis: Modifying splice site usage by changing the mRNP code, while maintaining the genetic code
Description:

Collection of functions to calculate a nucleotide sequence surrounding for splice donors sites to either activate or repress donor usage. The proposed alternative nucleotide sequence encodes the same amino acid and could be applied e.g. in reporter systems to silence or activate cryptic splice donor sites.

r-mcbiclust 1.34.0
Propagated dependencies: r-wgcna@1.73 r-scales@1.4.0 r-org-hs-eg-db@3.22.0 r-go-db@3.22.0 r-ggplot2@4.0.1 r-ggally@2.4.0 r-cluster@2.1.8.1 r-biocparallel@1.44.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MCbiclust
Licenses: GPL 2
Build system: r
Synopsis: Massive correlating biclusters for gene expression data and associated methods
Description:

Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.

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-mvoutdata 1.46.0
Propagated dependencies: r-lumi@2.62.0 r-biobase@2.70.0 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mvoutData
Licenses: Artistic License 2.0
Build system: r
Synopsis: affy and illumina raw data for assessing outlier detector performance
Description:

affy and illumina raw data for assessing outlier detector performance.

r-moe430aprobe 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/moe430aprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type moe430a
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 MOE430A\_probe\_tab.

r-multigsea 1.20.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/yigbt/multiGSEA
Licenses: GPL 3
Build system: r
Synopsis: Combining GSEA-based pathway enrichment with multi omics data integration
Description:

Extracted features from pathways derived from 8 different databases (KEGG, Reactome, Biocarta, etc.) can be used on transcriptomic, proteomic, and/or metabolomic level to calculate a combined GSEA-based enrichment score.

r-mistyr 1.18.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://saezlab.github.io/mistyR/
Licenses: GPL 3
Build system: r
Synopsis: Multiview Intercellular SpaTial modeling framework
Description:

mistyR is an implementation of the Multiview Intercellular SpaTialmodeling framework (MISTy). MISTy is an explainable machine learning framework for knowledge extraction and analysis of single-cell, highly multiplexed, spatially resolved data. MISTy facilitates an in-depth understanding of marker interactions by profiling the intra- and intercellular relationships. MISTy is a flexible framework able to process a custom number of views. Each of these views can describe a different spatial context, i.e., define a relationship among the observed expressions of the markers, such as intracellular regulation or paracrine regulation, but also, the views can also capture cell-type specific relationships, capture relations between functional footprints or focus on relations between different anatomical regions. Each MISTy view is considered as a potential source of variability in the measured marker expressions. Each MISTy view is then analyzed for its contribution to the total expression of each marker and is explained in terms of the interactions with other measurements that led to the observed contribution.

r-mgsa 1.58.0
Propagated dependencies: r-gplots@3.2.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/sba1/mgsa-bioc
Licenses: Artistic License 2.0
Build system: r
Synopsis: Model-based gene set analysis
Description:

Model-based Gene Set Analysis (MGSA) is a Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology.

r-mudata 1.14.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-s4vectors@0.48.0 r-rhdf5@2.54.0 r-multiassayexperiment@1.36.1 r-matrix@1.7-4 r-delayedarray@0.36.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/ilia-kats/MuData
Licenses: GPL 3
Build system: r
Synopsis: Serialization for MultiAssayExperiment Objects
Description:

Save MultiAssayExperiments to h5mu files supported by muon and mudata. Muon is a Python framework for multimodal omics data analysis. It uses an HDF5-based format for data storage.

r-mgug4120a-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/mgug4120a.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Agilent annotation data (chip mgug4120a)
Description:

Agilent annotation data (chip mgug4120a) assembled using data from public repositories.

r-moleculeexperiment 1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/SydneyBioX/MoleculeExperiment
Licenses: Expat
Build system: r
Synopsis: Prioritising a molecule-level storage of Spatial Transcriptomics Data
Description:

MoleculeExperiment contains functions to create and work with objects from the new MoleculeExperiment class. We introduce this class for analysing molecule-based spatial transcriptomics data (e.g., Xenium by 10X, Cosmx SMI by Nanostring, and Merscope by Vizgen). This allows researchers to analyse spatial transcriptomics data at the molecule level, and to have standardised data formats accross vendors.

r-methodical 1.6.0
Dependencies: kallisto@0.50.1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/richardheery/methodical
Licenses: GPL 3+
Build system: r
Synopsis: Discovering genomic regions where methylation is strongly associated with transcriptional activity
Description:

DNA methylation is generally considered to be associated with transcriptional silencing. However, comprehensive, genome-wide investigation of this relationship requires the evaluation of potentially millions of correlation values between the methylation of individual genomic loci and expression of associated transcripts in a relatively large numbers of samples. Methodical makes this process quick and easy while keeping a low memory footprint. It also provides a novel method for identifying regions where a number of methylation sites are consistently strongly associated with transcriptional expression. In addition, Methodical enables housing DNA methylation data from diverse sources (e.g. WGBS, RRBS and methylation arrays) with a common framework, lifting over DNA methylation data between different genome builds and creating base-resolution plots of the association between DNA methylation and transcriptional activity at transcriptional start sites.

r-mai 1.16.0
Propagated dependencies: r-tidyverse@2.0.0 r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-pcamethods@2.2.0 r-missforest@1.6.1 r-future-apply@1.20.0 r-future@1.68.0 r-foreach@1.5.2 r-e1071@1.7-16 r-doparallel@1.0.17 r-caret@7.0-1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/KechrisLab/MAI
Licenses: GPL 3
Build system: r
Synopsis: Mechanism-Aware Imputation
Description:

This package provides a two-step approach to imputing missing data in metabolomics. Step 1 uses a random forest classifier to classify missing values as either Missing Completely at Random/Missing At Random (MCAR/MAR) or Missing Not At Random (MNAR). MCAR/MAR are combined because it is often difficult to distinguish these two missing types in metabolomics data. Step 2 imputes the missing values based on the classified missing mechanisms, using the appropriate imputation algorithms. Imputation algorithms tested and available for MCAR/MAR include Bayesian Principal Component Analysis (BPCA), Multiple Imputation No-Skip K-Nearest Neighbors (Multi_nsKNN), and Random Forest. Imputation algorithms tested and available for MNAR include nsKNN and a single imputation approach for imputation of metabolites where left-censoring is present.

r-matrixrider 1.42.0
Propagated dependencies: r-xvector@0.50.0 r-tfbstools@1.48.0 r-s4vectors@0.48.0 r-iranges@2.44.0 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MatrixRider
Licenses: GPL 3
Build system: r
Synopsis: Obtain total affinity and occupancies for binding site matrices on a given sequence
Description:

Calculates a single number for a whole sequence that reflects the propensity of a DNA binding protein to interact with it. The DNA binding protein has to be described with a PFM matrix, for example gotten from Jaspar.

r-multimodalexperiment 1.10.0
Propagated dependencies: r-s4vectors@0.48.0 r-multiassayexperiment@1.36.1 r-iranges@2.44.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MultimodalExperiment
Licenses: Artistic License 2.0
Build system: r
Synopsis: Integrative Bulk and Single-Cell Experiment Container
Description:

MultimodalExperiment is an S4 class that integrates bulk and single-cell experiment data; it is optimally storage-efficient, and its methods are exceptionally fast. It effortlessly represents multimodal data of any nature and features normalized experiment, subject, sample, and cell annotations, which are related to underlying biological experiments through maps. Its coordination methods are opt-in and employ database-like join operations internally to deliver fast and flexible management of multimodal data.

r-malaria-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/malaria.db0
Licenses: Artistic License 2.0
Build system: r
Synopsis: Base Level Annotation databases for malaria
Description:

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

Total results: 2911