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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-impcdata 1.46.0
Propagated dependencies: r-rjson@0.2.23
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/IMPCdata
Licenses: FSDG-compatible
Build system: r
Synopsis: Retrieves data from IMPC database
Description:

Package contains methods for data retrieval from IMPC Database.

r-illuminahumanmethylation27k-db 1.4.8
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/IlluminaHumanMethylation27k.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina Illumina Human Methylation 27k annotation data (chip IlluminaHumanMethylation27k)
Description:

Illumina Illumina Human Methylation 27k annotation data (chip IlluminaHumanMethylation27k) assembled using data from public repositories.

r-iggeneusage 1.24.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/snaketron/IgGeneUsage
Licenses: Expat
Build system: r
Synopsis: Differential gene usage in immune repertoires
Description:

Detection of biases in the usage of immunoglobulin (Ig) genes is an important task in immune repertoire profiling. IgGeneUsage detects aberrant Ig gene usage between biological conditions using a probabilistic model which is analyzed computationally by Bayes inference. With this IgGeneUsage also avoids some common problems related to the current practice of null-hypothesis significance testing.

r-iseeu 1.22.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-shinyace@0.4.4 r-shiny@1.11.1 r-s4vectors@0.48.0 r-iseehex@1.12.0 r-isee@2.22.0 r-iranges@2.44.0 r-ggplot2@4.0.1 r-dt@0.34.0 r-colourpicker@1.3.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/iSEE/iSEEu
Licenses: Expat
Build system: r
Synopsis: iSEE Universe
Description:

iSEEu (the iSEE universe) contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels, or modes allowing easy configuration of iSEE applications.

r-ideal 2.4.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/federicomarini/ideal
Licenses: Expat
Build system: r
Synopsis: Interactive Differential Expression AnaLysis
Description:

This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package. Support for reproducibility of the whole analysis is provided by means of a template report which gets automatically compiled and can be stored/shared.

r-illuminaratv1-db 1.26.0
Propagated dependencies: r-org-rn-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/illuminaRatv1.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina Ratv1 annotation data (chip illuminaRatv1)
Description:

Illumina Ratv1 annotation data (chip illuminaRatv1) assembled using data from public repositories.

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-isobayes 1.8.0
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-ipddb 1.28.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/DKMS-LSL/ipdDb
Licenses: Artistic License 2.0
Build system: r
Synopsis: IPD IMGT/HLA and IPD KIR database for Homo sapiens
Description:

All alleles from the IPD IMGT/HLA <https://www.ebi.ac.uk/ipd/imgt/hla/> and IPD KIR <https://www.ebi.ac.uk/ipd/kir/> database for Homo sapiens. Reference: Robinson J, Maccari G, Marsh SGE, Walter L, Blokhuis J, Bimber B, Parham P, De Groot NG, Bontrop RE, Guethlein LA, and Hammond JA KIR Nomenclature in non-human species Immunogenetics (2018), in preparation.

r-isolde 1.38.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: www.r-project.org
Licenses: GPL 2+
Build system: r
Synopsis: Integrative Statistics of alleLe Dependent Expression
Description:

This package provides ISoLDE a new method for identifying imprinted genes. This method is dedicated to data arising from RNA sequencing technologies. The ISoLDE package implements original statistical methodology described in the publication below.

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-ibbig 1.54.0
Propagated dependencies: r-xtable@1.8-4 r-biclust@2.0.3.1 r-ade4@1.7-23
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: http://bcb.dfci.harvard.edu/~aedin/publications/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Iterative Binary Biclustering of Genesets
Description:

iBBiG is a bi-clustering algorithm which is optimizes for binary data analysis. We apply it to meta-gene set analysis of large numbers of gene expression datasets. The iterative algorithm extracts groups of phenotypes from multiple studies that are associated with similar gene sets. iBBiG does not require prior knowledge of the number or scale of clusters and allows discovery of clusters with diverse sizes.

r-illuminahumanmethylationmsaanno-ilm10a1-hg38 0.1.0
Propagated dependencies: r-minfi@1.56.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/jmacdon/IlluminaHumanMethylationMSAanno.ilm10a1.hg38
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation for Illumina's MSA methylation arrays
Description:

An annotation package for Illumina's MSA methylation arrays.

r-intansv 1.50.0
Propagated dependencies: r-plyr@1.8.9 r-iranges@2.44.0 r-ggbio@1.58.0 r-genomicranges@1.62.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/intansv
Licenses: Expat
Build system: r
Synopsis: Integrative analysis of structural variations
Description:

This package provides efficient tools to read and integrate structural variations predicted by popular softwares. Annotation and visulation of structural variations are also implemented in the package.

r-inpas 2.18.1
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-iasva 1.28.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-irlba@2.3.5.1 r-cluster@2.1.8.1 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/iasva
Licenses: GPL 2
Build system: r
Synopsis: Iteratively Adjusted Surrogate Variable Analysis
Description:

Iteratively Adjusted Surrogate Variable Analysis (IA-SVA) is a statistical framework to uncover hidden sources of variation even when these sources are correlated. IA-SVA provides a flexible methodology to i) identify a hidden factor for unwanted heterogeneity while adjusting for all known factors; ii) test the significance of the putative hidden factor for explaining the unmodeled variation in the data; and iii), if significant, use the estimated factor as an additional known factor in the next iteration to uncover further hidden factors.

r-intramirexplorer 1.32.0
Propagated dependencies: r-knitr@1.50 r-igraph@2.2.1 r-fgnet@3.44.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/VilainLab/IntramiRExploreR
Licenses: GPL 2
Build system: r
Synopsis: Predicting Targets for Drosophila Intragenic miRNAs
Description:

Intra-miR-ExploreR, an integrative miRNA target prediction bioinformatics tool, identifies targets combining expression and biophysical interactions of a given microRNA (miR). Using the tool, we have identified targets for 92 intragenic miRs in D. melanogaster, using available microarray expression data, from Affymetrix 1 and Affymetrix2 microarray array platforms, providing a global perspective of intragenic miR targets in Drosophila. Predicted targets are grouped according to biological functions using the DAVID Gene Ontology tool and are ranked based on a biologically relevant scoring system, enabling the user to identify functionally relevant targets for a given miR.

r-isomirs 1.38.1
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/isomiRs
Licenses: Expat
Build system: r
Synopsis: Analyze isomiRs and miRNAs from small RNA-seq
Description:

Characterization of miRNAs and isomiRs, clustering and differential expression.

r-ihwpaper 1.38.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-rcpp@1.1.0 r-qvalue@2.42.0 r-ihw@1.38.0 r-ggplot2@4.0.1 r-genefilter@1.92.0 r-fdrtool@1.2.18 r-dplyr@1.1.4 r-deseq2@1.50.2 r-cowplot@1.2.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/IHWpaper
Licenses: Artistic License 2.0
Build system: r
Synopsis: Reproduce figures in IHW paper
Description:

This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885) and the data analysis in https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12411, cf. the arXiv preprint (http://arxiv.org/abs/1701.05179). Thus it is a companion package to the Bioconductor IHW package.

r-iseeindex 1.8.0
Propagated dependencies: r-urltools@1.7.3.1 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-singlecellexperiment@1.32.0 r-shinyjs@2.1.0 r-shinydashboard@0.7.3 r-shiny@1.11.1 r-rintrojs@0.3.4 r-paws-storage@0.9.0 r-isee@2.22.0 r-dt@0.34.0 r-biocfilecache@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/iSEE/iSEEindex
Licenses: Artistic License 2.0
Build system: r
Synopsis: iSEE extension for a landing page to a custom collection of data sets
Description:

This package provides an interface to any collection of data sets within a single iSEE web-application. The main functionality of this package is to define a custom landing page allowing app maintainers to list a custom collection of data sets that users can selected from and directly load objects into an iSEE web-application.

r-illuminahumanv2beadid-db 1.8.0
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/illuminaHumanv2BeadID.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina HumanWGv2 annotation data (chip illuminaHumanv2BeadID)
Description:

Illumina HumanWGv2 annotation data (chip illuminaHumanv2BeadID) assembled using data from public repositories to be used with data summarized from bead-level data with numeric ArrayAddressIDs as keys. Illumina probes with a No match or Bad quality score were removed prior to annotation. See http://www.compbio.group.cam.ac.uk/Resources/Annotation/index.html and Barbosa-Morais et al (2010) A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Research.

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-idpr 1.20.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/idpr
Licenses: LGPL 3+
Build system: r
Synopsis: Profiling and Analyzing Intrinsically Disordered Proteins in R
Description:

‘idpr’ aims to integrate tools for the computational analysis of intrinsically disordered proteins (IDPs) within R. This package is used to identify known characteristics of IDPs for a sequence of interest with easily reported and dynamic results. Additionally, this package includes tools for IDP-based sequence analysis to be used in conjunction with other R packages. Described in McFadden WM & Yanowitz JL (2022). "idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in R." PloS one, 17(4), e0266929. <https://doi.org/10.1371/journal.pone.0266929>.

r-imcrtools 1.16.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/BodenmillerGroup/imcRtools
Licenses: GPL 3
Build system: r
Synopsis: Methods for imaging mass cytometry data analysis
Description:

This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected.

Total results: 2911