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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-multirnaflow 1.8.0
Propagated dependencies: r-upsetr@1.4.0 r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-rlang@1.1.6 r-reshape2@1.4.5 r-plot3drgl@1.0.5 r-plot3d@1.4.2 r-mfuzz@2.70.0 r-gprofiler2@0.2.4 r-ggrepel@0.9.6 r-ggplotify@0.1.3 r-ggplot2@4.0.1 r-ggalluvial@0.12.5 r-factominer@2.12 r-factoextra@1.0.7 r-deseq2@1.50.2 r-complexheatmap@2.26.0 r-biobase@2.70.0
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-msqc1 1.38.0
Propagated dependencies: r-lattice@0.22-7
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://panoramaweb.org/labkey/MSQC1.url
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: Sigma mix MSQC1 data
Description:

contains eight technical replicate data set and a three replicate dilution series of the MS Qual/Quant Quality Control Mix standard sample (Sigma-Aldrich, Buchs, Switzerland) measured on five different mass spectrometer platforms at the Functional Genomics Center Zurich.

r-m10kcod-db 3.4.0
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/m10kcod.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Codelink UniSet Mouse I Bioarray (~10 000 mouse gene targets) annotation data (chip m10kcod)
Description:

Codelink UniSet Mouse I Bioarray (~10 000 mouse gene targets) annotation data (chip m10kcod) assembled using data from public repositories.

r-mu6500subacdf 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/mu6500subacdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: mu6500subacdf
Description:

This package provides a package containing an environment representing the Mu6500subA.CDF file.

r-minimumdistance 1.54.0
Propagated dependencies: r-vanillaice@1.72.0 r-summarizedexperiment@1.40.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-oligoclasses@1.72.0 r-matrixstats@1.5.0 r-matrixgenerics@1.22.0 r-lattice@0.22-7 r-iranges@2.44.0 r-genomicranges@1.62.0 r-foreach@1.5.2 r-ff@4.5.2 r-dnacopy@1.84.0 r-data-table@1.17.8 r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MinimumDistance
Licenses: Artistic License 2.0
Build system: r
Synopsis: Package for De Novo CNV Detection in Case-Parent Trios
Description:

Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.

r-matrixqcvis 1.18.0
Propagated dependencies: r-vsn@3.78.0 r-upsetr@1.4.0 r-umap@0.2.10.0 r-tidyr@1.3.1 r-tibble@3.3.0 r-sva@3.58.0 r-summarizedexperiment@1.40.0 r-shinyjs@2.1.0 r-shinyhelper@0.3.2 r-shinydashboard@0.7.3 r-shiny@1.11.1 r-rtsne@0.17 r-rmarkdown@2.30 r-rlang@1.1.6 r-proda@1.24.0 r-plotly@4.11.0 r-pcamethods@2.2.0 r-mass@7.3-65 r-limma@3.66.0 r-imputelcmd@2.1 r-impute@1.84.0 r-htmlwidgets@1.6.4 r-hmisc@5.2-4 r-ggplot2@4.0.1 r-experimenthub@3.0.0 r-dt@0.34.0 r-dplyr@1.1.4 r-complexheatmap@2.26.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MatrixQCvis
Licenses: GPL 3
Build system: r
Synopsis: Shiny-based interactive data-quality exploration for omics data
Description:

Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. We present here the MatrixQCvis package, which provides shiny-based interactive visualization of data quality metrics at the per-sample and per-feature level. It is broadly applicable to quantitative omics data types that come in matrix-like format (features x samples). It enables the detection of low-quality samples, drifts, outliers and batch effects in data sets. Visualizations include amongst others bar- and violin plots of the (count/intensity) values, mean vs standard deviation plots, MA plots, empirical cumulative distribution function (ECDF) plots, visualizations of the distances between samples, and multiple types of dimension reduction plots. Furthermore, MatrixQCvis allows for differential expression analysis based on the limma (moderated t-tests) and proDA (Wald tests) packages. MatrixQCvis builds upon the popular Bioconductor SummarizedExperiment S4 class and enables thus the facile integration into existing workflows. The package is especially tailored towards metabolomics and proteomics mass spectrometry data, but also allows to assess the data quality of other data types that can be represented in a SummarizedExperiment object.

r-measurementerror-cor 1.82.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MeasurementError.cor
Licenses: LGPL 2.0+
Build system: r
Synopsis: Measurement Error model estimate for correlation coefficient
Description:

Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation.

r-msbackendmetabolights 1.4.2
Propagated dependencies: r-spectra@1.20.0 r-s4vectors@0.48.0 r-protgenerics@1.42.0 r-progress@1.2.3 r-curl@7.0.0 r-biocfilecache@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/RforMassSpectrometry/MsBackendMetaboLights
Licenses: Artistic License 2.0
Build system: r
Synopsis: Retrieve Mass Spectrometry Data from MetaboLights
Description:

MetaboLights is one of the main public repositories for storage of metabolomics experiments, which includes analysis results as well as raw data. The MsBackendMetaboLights package provides functionality to retrieve and represent mass spectrometry (MS) data from MetaboLights. Data files are downloaded and cached locally avoiding repetitive downloads. MS data from metabolomics experiments can thus be directly and seamlessly integrated into R-based analysis workflows with the Spectra and MsBackendMetaboLights package.

r-mu11ksubaprobe 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/mu11ksubaprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type mu11ksuba
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 Mu11KsubA\_probe\_tab.

r-micsqtl 1.8.0
Propagated dependencies: r-toast@1.24.0 r-tca@1.2.1 r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-purrr@1.2.0 r-nnls@1.6 r-magrittr@2.0.4 r-glue@1.8.0 r-ggridges@0.5.7 r-ggpubr@0.6.2 r-ggplot2@4.0.1 r-dirmult@0.1.3-5 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MICSQTL
Licenses: GPL 3
Build system: r
Synopsis: MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)
Description:

Our pipeline, MICSQTL, utilizes scRNA-seq reference and bulk transcriptomes to estimate cellular composition in the matched bulk proteomes. The expression of genes and proteins at either bulk level or cell type level can be integrated by Angle-based Joint and Individual Variation Explained (AJIVE) framework. Meanwhile, MICSQTL can perform cell-type-specic quantitative trait loci (QTL) mapping to proteins or transcripts based on the input of bulk expression data and the estimated cellular composition per molecule type, without the need for single cell sequencing. We use matched transcriptome-proteome from human brain frontal cortex tissue samples to demonstrate the input and output of our tool.

r-mu11ksubacdf 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/mu11ksubacdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: mu11ksubacdf
Description:

This package provides a package containing an environment representing the Mu11KsubA.CDF file.

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-mouse4302barcodevecs 1.48.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mouse4302barcodevecs
Licenses: GPL 2+
Build system: r
Synopsis: mouse4302 data for barcode
Description:

Data used by the barcode package for microarrays of type mouse4302.

r-mbpcr 1.64.0
Propagated dependencies: r-oligoclasses@1.72.0 r-gwastools@1.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://www.idsia.ch/~paola/mBPCR
Licenses: GPL 2+
Build system: r
Synopsis: Bayesian Piecewise Constant Regression for DNA copy number estimation
Description:

It contains functions for estimating the DNA copy number profile using mBPCR with the aim of detecting regions with copy number changes.

r-methrix 1.24.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-matrixstats@1.5.0 r-iranges@2.44.0 r-hdf5array@1.38.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-delayedmatrixstats@1.32.0 r-delayedarray@0.36.0 r-data-table@1.17.8 r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/CompEpigen/methrix
Licenses: Expat
Build system: r
Synopsis: Fast and efficient summarization of generic bedGraph files from Bisufite sequencing
Description:

Bedgraph files generated by Bisulfite pipelines often come in various flavors. Critical downstream step requires summarization of these files into methylation/coverage matrices. This step of data aggregation is done by Methrix, including many other useful downstream functions.

r-matchbox 1.52.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/matchBox
Licenses: Artistic License 2.0
Build system: r
Synopsis: Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis
Description:

The matchBox package enables comparing ranked vectors of features, merging multiple datasets, removing redundant features, using CAT-plots and Venn diagrams, and computing statistical significance.

r-mwastools 1.34.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-rcurl@1.98-1.17 r-qvalue@2.42.0 r-ppcor@1.1 r-keggrest@1.50.0 r-kegggraph@1.70.0 r-igraph@2.2.1 r-gridextra@2.3 r-glm2@1.2.1 r-ggplot2@4.0.1 r-complexheatmap@2.26.0 r-car@3.1-3 r-boot@1.3-32
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MWASTools
Licenses: FSDG-compatible
Build system: r
Synopsis: MWASTools: an integrated pipeline to perform metabolome-wide association studies
Description:

MWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results.

r-merfishdata 1.12.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-spatialexperiment@1.20.0 r-singlecellexperiment@1.32.0 r-s4vectors@0.48.0 r-hdf5array@1.38.0 r-experimenthub@3.0.0 r-ebimage@4.52.0 r-bumpymatrix@1.18.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/ccb-hms/MerfishData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Collection of public MERFISH datasets
Description:

MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis.

r-methylmix 2.40.0
Propagated dependencies: r-rpmm@1.25 r-rcurl@1.98-1.17 r-rcolorbrewer@1.1-3 r-r-matlab@3.7.0 r-limma@3.66.0 r-impute@1.84.0 r-ggplot2@4.0.1 r-foreach@1.5.2 r-digest@0.6.39 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/MethylMix
Licenses: GPL 2
Build system: r
Synopsis: MethylMix: Identifying methylation driven cancer genes
Description:

MethylMix is an algorithm implemented to identify hyper and hypomethylated genes for a disease. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix uses a novel statistic, the Differential Methylation value or DM-value defined as the difference of a methylation state with the normal methylation state. Finally, matched gene expression data is used to identify, besides differential, functional methylation states by focusing on methylation changes that effect gene expression. References: Gevaert 0. MethylMix: an R package for identifying DNA methylation-driven genes. Bioinformatics (Oxford, England). 2015;31(11):1839-41. doi:10.1093/bioinformatics/btv020. Gevaert O, Tibshirani R, Plevritis SK. Pancancer analysis of DNA methylation-driven genes using MethylMix. Genome Biology. 2015;16(1):17. doi:10.1186/s13059-014-0579-8.

r-msstatsresponse 1.0.0
Propagated dependencies: r-ggplot2@4.0.1 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/Vitek-Lab/MSstatsResponse
Licenses: Artistic License 2.0
Build system: r
Synopsis: Statistical Methods for Chemoproteomics Dose-Response Analysis
Description:

This package provides tools for detecting drug-protein interactions and estimating IC50 values from chemoproteomics data. Implements semi-parametric isotonic regression, bootstrapping, and curve fitting to evaluate compound effects on protein abundance.

r-moleculeexperiment 1.10.0
Propagated dependencies: r-terra@1.8-86 r-spatialexperiment@1.20.0 r-s4vectors@0.48.0 r-rlang@1.1.6 r-rjson@0.2.23 r-rhdf5@2.54.0 r-purrr@1.2.0 r-matrix@1.7-4 r-magrittr@2.0.4 r-ggplot2@4.0.1 r-ebimage@4.52.0 r-dplyr@1.1.4 r-data-table@1.17.8 r-cli@3.6.5 r-biocparallel@1.44.0
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-meshr 2.16.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-rmarkdown@2.30 r-meshdbi@1.46.0 r-markdown@2.0 r-knitr@1.50 r-fdrtool@1.2.18 r-category@2.76.0 r-biocstyle@2.38.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/meshr
Licenses: Artistic License 2.0
Build system: r
Synopsis: Tools for conducting enrichment analysis of MeSH
Description:

This package provides a set of annotation maps describing the entire MeSH assembled using data from MeSH.

r-mosaicsexample 1.48.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://groups.google.com/group/mosaics_user_group
Licenses: GPL 2+
Build system: r
Synopsis: Example data for the mosaics package, which implements MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data for transcription factor binding and histone modification
Description:

Data for the mosaics package, consisting of (1) chromosome 22 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding and H3K4me3 modification in MCF7 cell line from ENCODE database (HG19) and (2) chromosome 21 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding, with mappability, GC content, and sequence ambiguity scores of human genome HG18.

r-mu19ksubccdf 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/mu19ksubccdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: mu19ksubccdf
Description:

This package provides a package containing an environment representing the Mu19KsubC.CDF file.

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