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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-indeed 2.24.0
Propagated dependencies: r-visnetwork@2.1.4 r-igraph@2.2.1 r-glasso@1.11 r-devtools@2.4.6
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: http://github.com/ressomlab/INDEED
Licenses: Artistic License 2.0
Build system: r
Synopsis: Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
Description:

An R package for integrated differential expression and differential network analysis based on omic data for cancer biomarker discovery. Both correlation and partial correlation can be used to generate differential network to aid the traditional differential expression analysis to identify changes between biomolecules on both their expression and pairwise association levels. A detailed description of the methodology has been published in Methods journal (PMID: 27592383). An interactive visualization feature allows for the exploration and selection of candidate biomarkers.

r-islet 1.12.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-purrr@1.2.0 r-nnls@1.6 r-matrix@1.7-4 r-lme4@1.1-37 r-biocparallel@1.44.0 r-biocgenerics@0.56.0 r-abind@1.4-8
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/ISLET
Licenses: GPL 2
Build system: r
Synopsis: Individual-Specific ceLl typE referencing Tool
Description:

ISLET is a method to conduct signal deconvolution for general -omics data. It can estimate the individual-specific and cell-type-specific reference panels, when there are multiple samples observed from each subject. It takes the input of the observed mixture data (feature by sample matrix), and the cell type mixture proportions (sample by cell type matrix), and the sample-to-subject information. It can solve for the reference panel on the individual-basis and conduct test to identify cell-type-specific differential expression (csDE) genes. It also improves estimated cell type mixture proportions by integrating personalized reference panels.

r-imcdatasets 1.18.0
Propagated dependencies: 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-delayedarray@0.36.0 r-cytomapper@1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/BodenmillerGroup/imcdatasets
Licenses: FSDG-compatible
Build system: r
Synopsis: Collection of publicly available imaging mass cytometry (IMC) datasets
Description:

The imcdatasets package provides access to publicly available IMC datasets. IMC is a technology that enables measurement of > 40 proteins from tissue sections. The generated images can be segmented to extract single cell data. Datasets typically consist of three elements: a SingleCellExperiment object containing single cell data, a CytoImageList object containing multichannel images and a CytoImageList object containing the cell masks that were used to extract the single cell data from the images.

r-iseefier 1.6.0
Propagated dependencies: r-visnetwork@2.1.4 r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-rlang@1.1.6 r-iseeu@1.22.0 r-isee@2.22.0 r-igraph@2.2.1 r-ggplot2@4.0.1 r-biocbaseutils@1.12.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/NajlaAbassi/iSEEfier
Licenses: Expat
Build system: r
Synopsis: Streamlining the creation of initial states for starting an iSEE instance
Description:

iSEEfier provides a set of functionality to quickly and intuitively create, inspect, and combine initial configuration objects. These can be conveniently passed in a straightforward manner to the function call to launch iSEE() with the specified configuration. This package currently works seamlessly with the sets of panels provided by the iSEE and iSEEu packages, but can be extended to accommodate the usage of any custom panel (e.g. from iSEEde, iSEEpathways, or any panel developed independently by the user).

r-immunoclust 1.42.0
Dependencies: gsl@2.8
Propagated dependencies: r-lattice@0.22-7 r-flowcore@2.22.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/immunoClust
Licenses: Artistic License 2.0
Build system: r
Synopsis: immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
Description:

immunoClust is a model based clustering approach for Flow Cytometry samples. The cell-events of single Flow Cytometry samples are modelled by a mixture of multinominal normal- or t-distributions. The cell-event clusters of several samples are modelled by a mixture of multinominal normal-distributions aiming stable co-clusters across these samples.

r-igvr 1.30.0
Propagated dependencies: r-variantannotation@1.56.0 r-rtracklayer@1.70.0 r-rcolorbrewer@1.1-3 r-httr@1.4.7 r-httpuv@1.6.16 r-genomicranges@1.62.0 r-genomicalignments@1.46.0 r-browserviz@2.32.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://gladkia.github.io/igvR/
Licenses: Expat
Build system: r
Synopsis: igvR: integrative genomics viewer
Description:

Access to igv.js, the Integrative Genomics Viewer running in a web browser.

r-ifaa 1.12.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-s4vectors@0.48.0 r-parallelly@1.45.1 r-matrixextra@0.1.15 r-matrix@1.7-4 r-mathjaxr@1.8-0 r-hdci@1.0-2 r-glmnet@4.1-10 r-foreach@1.5.2 r-dorng@1.8.6.2 r-doparallel@1.0.17 r-desctools@0.99.60
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://pubmed.ncbi.nlm.nih.gov/35241863/
Licenses: GPL 2
Build system: r
Synopsis: Robust Inference for Absolute Abundance in Microbiome Analysis
Description:

This package offers a robust approach to make inference on the association of covariates with the absolute abundance (AA) of microbiome in an ecosystem. It can be also directly applied to relative abundance (RA) data to make inference on AA because the ratio of two RA is equal to the ratio of their AA. This algorithm can estimate and test the associations of interest while adjusting for potential confounders. The estimates of this method have easy interpretation like a typical regression analysis. High-dimensional covariates are handled with regularization and it is implemented by parallel computing. False discovery rate is automatically controlled by this approach. Zeros do not need to be imputed by a positive value for the analysis. The IFAA package also offers the MZILN function for estimating and testing associations of abundance ratios with covariates.

r-iseepathways 1.8.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-shinywidgets@0.9.0 r-shiny@1.11.1 r-s4vectors@0.48.0 r-isee@2.22.0 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/iSEE/iSEEpathways
Licenses: Artistic License 2.0
Build system: r
Synopsis: iSEE extension for panels related to pathway analysis
Description:

This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of pathway analysis results. This package does not perform pathway analysis. Instead, it provides methods to embed precomputed pathway analysis results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.

r-igblastr 1.0.11
Propagated dependencies: r-xtable@1.8-4 r-xml2@1.5.0 r-tibble@3.3.0 r-s4vectors@0.48.0 r-rvest@1.0.5 r-r-utils@2.13.0 r-jsonlite@2.0.0 r-iranges@2.44.0 r-httr@1.4.7 r-genomeinfodb@1.46.0 r-curl@7.0.0 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/igblastr
Licenses: Artistic License 2.0
Build system: r
Synopsis: User-friendly R Wrapper to IgBLAST
Description:

The igblastr package provides functions to conveniently install and use a local IgBLAST installation from within R. IgBLAST is described at <https://pubmed.ncbi.nlm.nih.gov/23671333/>. IgBLAST web interface: <https://www.ncbi.nlm.nih.gov/igblast/>.

r-immunotation 1.18.0
Propagated dependencies: r-xml2@1.5.0 r-tidyr@1.3.1 r-stringr@1.6.0 r-rvest@1.0.5 r-rlang@1.1.6 r-readr@2.1.6 r-ontologyindex@2.12 r-maps@3.4.3 r-ggplot2@4.0.1 r-curl@7.0.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/immunotation
Licenses: GPL 3
Build system: r
Synopsis: Tools for working with diverse immune genes
Description:

MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells. The repertoire of antigens presented in a given genetic background largely depends on the sequence of the encoded MHC molecules, and thus, in humans, on the highly variable HLA (human leukocyte antigen) genes of the hyperpolymorphic HLA locus. More than 28,000 different HLA alleles have been reported, with significant differences in allele frequencies between human populations worldwide. Reproducible and consistent annotation of HLA alleles in large-scale bioinformatics workflows remains challenging, because the available reference databases and software tools often use different HLA naming schemes. The package immunotation provides tools for consistent annotation of HLA genes in typical immunoinformatics workflows such as for example the prediction of MHC-presented peptides in different human donors. Converter functions that provide mappings between different HLA naming schemes are based on the MHC restriction ontology (MRO). The package also provides automated access to HLA alleles frequencies in worldwide human reference populations stored in the Allele Frequency Net Database.

r-isobayes 1.8.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-rcpparmadillo@15.2.2-1 r-rcpp@1.1.0 r-iterators@1.0.14 r-hdinterval@0.2.4 r-glue@1.8.0 r-ggplot2@4.0.1 r-foreach@1.5.2 r-dorng@1.8.6.2 r-doparallel@1.0.17 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/SimoneTiberi/IsoBayes
Licenses: GPL 3
Build system: r
Synopsis: IsoBayes: Single Isoform protein inference Method via Bayesian Analyses
Description:

IsoBayes is a Bayesian method to perform inference on single protein isoforms. Our approach infers the presence/absence of protein isoforms, and also estimates their abundance; additionally, it provides a measure of the uncertainty of these estimates, via: i) the posterior probability that a protein isoform is present in the sample; ii) a posterior credible interval of its abundance. IsoBayes inputs liquid cromatography mass spectrometry (MS) data, and can work with both PSM counts, and intensities. When available, trascript isoform abundances (i.e., TPMs) are also incorporated: TPMs are used to formulate an informative prior for the respective protein isoform relative abundance. We further identify isoforms where the relative abundance of proteins and transcripts significantly differ. We use a two-layer latent variable approach to model two sources of uncertainty typical of MS data: i) peptides may be erroneously detected (even when absent); ii) many peptides are compatible with multiple protein isoforms. In the first layer, we sample the presence/absence of each peptide based on its estimated probability of being mistakenly detected, also known as PEP (i.e., posterior error probability). In the second layer, for peptides that were estimated as being present, we allocate their abundance across the protein isoforms they map to. These two steps allow us to recover the presence and abundance of each protein isoform.

r-imman 1.30.0
Propagated dependencies: r-stringdb@2.22.0 r-seqinr@4.2-36 r-pwalign@1.6.0 r-igraph@2.2.1
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/IMMAN
Licenses: Artistic License 2.0
Build system: r
Synopsis: Interlog protein network reconstruction by Mapping and Mining ANalysis
Description:

Reconstructing Interlog Protein Network (IPN) integrated from several Protein protein Interaction Networks (PPINs). Using this package, overlaying different PPINs to mine conserved common networks between diverse species will be applicable.

r-inpas 2.18.1
Propagated dependencies: r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-reshape2@1.4.5 r-readr@2.1.6 r-preprocesscore@1.72.0 r-plyranges@1.30.1 r-parallelly@1.45.1 r-magrittr@2.0.4 r-limma@3.66.0 r-iranges@2.44.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomeinfodb@1.46.0 r-future-apply@1.20.0 r-future@1.68.0 r-flock@0.7 r-dplyr@1.1.4 r-depmixs4@1.5-1 r-cleanupdtseq@1.48.0 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biobase@2.70.0 r-batchtools@0.9.18 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/InPAS
Licenses: GPL 2+
Build system: r
Synopsis: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
Description:

Alternative polyadenylation (APA) is one of the important post- transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites and the differential usage of APA sites from RNA-Seq data. It leverages cleanUpdTSeq to fine tune identified APA sites by removing false sites.

r-ipo 1.36.0
Propagated dependencies: r-xcms@4.8.0 r-rsm@2.10.6 r-camera@1.66.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/rietho/IPO
Licenses: FSDG-compatible
Build system: r
Synopsis: Automated Optimization of XCMS Data Processing parameters
Description:

The outcome of XCMS data processing strongly depends on the parameter settings. IPO (`Isotopologue Parameter Optimization`) is a parameter optimization tool that is applicable for different kinds of samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. IPO uses natural, stable 13C isotopes to calculate a peak picking score. Retention time correction is optimized by minimizing the relative retention time differences within features and grouping parameters are optimized by maximizing the number of features showing exactly one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiment. The resulting scores are evaluated using response surface models.

r-imagetcga 1.2.0
Propagated dependencies: r-viridis@0.6.5 r-tidyr@1.3.1 r-shiny@1.11.1 r-rlang@1.1.6 r-leaflet@2.2.3 r-ggplot2@4.0.1 r-dt@0.34.0 r-dplyr@1.1.4 r-clipr@0.8.0 r-bslib@0.9.0 r-bsicons@0.1.2
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/billila/imageTCGA
Licenses: Artistic License 2.0
Build system: r
Synopsis: TCGA Diagnostic Image Database Explorer
Description:

This package provides a Shiny application to explore the TCGA Diagnostic Image Database.

r-iseetree 1.4.0
Propagated dependencies: r-treesummarizedexperiment@2.18.0 r-tidygraph@1.3.1 r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-shinywidgets@0.9.0 r-shiny@1.11.1 r-s4vectors@0.48.0 r-purrr@1.2.0 r-miaviz@1.18.0 r-mia@1.18.0 r-isee@2.22.0 r-ggtree@4.0.1 r-ggplot2@4.0.1 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/microbiome/iSEEtree
Licenses: Artistic License 2.0
Build system: r
Synopsis: Interactive visualisation for microbiome data
Description:

iSEEtree is an extension of iSEE for the TreeSummarizedExperiment data container. It provides interactive panel designs to explore hierarchical datasets, such as the microbiome and cell lines.

r-illuminahumanwgdaslv4-db 1.26.0
Propagated dependencies: r-org-hs-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/illuminaHumanWGDASLv4.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina HumanWGDASLv4 annotation data (chip illuminaHumanWGDASLv4)
Description:

Illumina HumanWGDASLv4 annotation data (chip illuminaHumanWGDASLv4) assembled using data from public repositories.

r-illuminamousev1p1-db 1.26.0
Propagated dependencies: r-org-mm-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/illuminaMousev1p1.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina MouseWG6v1p1 annotation data (chip illuminaMousev1p1)
Description:

Illumina MouseWG6v1p1 annotation data (chip illuminaMousev1p1) assembled using data from public repositories.

r-idiogram 1.86.0
Propagated dependencies: r-plotrix@3.8-13 r-biobase@2.70.0 r-annotate@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/idiogram
Licenses: GPL 2
Build system: r
Synopsis: idiogram
Description:

This package provides a package for plotting genomic data by chromosomal location.

r-iaseq 1.54.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/iASeq
Licenses: GPL 2
Build system: r
Synopsis: iASeq: integrating multiple sequencing datasets for detecting allele-specific events
Description:

It fits correlation motif model to multiple RNAseq or ChIPseq studies to improve detection of allele-specific events and describe correlation patterns across studies.

r-iwtomics 1.34.1
Propagated dependencies: r-s4vectors@0.48.0 r-kernsmooth@2.23-26 r-iranges@2.44.0 r-gtable@0.3.6 r-genomicranges@1.62.0 r-fda@6.3.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/IWTomics
Licenses: FSDG-compatible
Build system: r
Synopsis: Interval-Wise Testing for Omics Data
Description:

Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.

r-illuminahumanmethylationepicanno-ilm10b3-hg19 0.6.0
Propagated dependencies: r-minfi@1.56.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bitbucket.com/kasperdanielhansen/Illumina_EPIC
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation for Illumina's EPIC methylation arrays
Description:

An annotation package for Illumina's EPIC methylation arrays.

r-immunogenviewer 1.4.0
Propagated dependencies: r-uniprot-ws@2.50.0 r-patchwork@1.3.2 r-jsonlite@2.0.0 r-httr@1.4.7 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/kathiwaury/immunogenViewer
Licenses: FSDG-compatible
Build system: r
Synopsis: Visualization and evaluation of protein immunogens
Description:

Plots protein properties and visualizes position of peptide immunogens within protein sequence. Allows evaluation of immunogens based on structural and functional annotations to infer suitability for antibody-based methods aiming to detect native proteins.

r-igvshiny 1.6.0
Propagated dependencies: r-shiny@1.11.1 r-randomcolor@1.1.0.1 r-jsonlite@2.0.0 r-httr@1.4.7 r-htmlwidgets@1.6.4 r-genomicranges@1.62.0 r-genomeinfodbdata@1.2.15 r-futile-logger@1.4.3 r-checkmate@2.3.3 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/gladkia/igvShiny
Licenses: Expat
Build system: r
Synopsis: igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)
Description:

This package is a wrapper of Integrative Genomics Viewer (IGV). It comprises an htmlwidget version of IGV. It can be used as a module in Shiny apps.

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