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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-isocorrector 1.28.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://genomics.ur.de/files/IsoCorrectoR/
Licenses: GPL 3
Build system: r
Synopsis: Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments
Description:

IsoCorrectoR performs the correction of mass spectrometry data from stable isotope labeling/tracing metabolomics experiments with regard to natural isotope abundance and tracer impurity. Data from both MS and MS/MS measurements can be corrected (with any tracer isotope: 13C, 15N, 18O...), as well as ultra-high resolution MS data from multiple-tracer experiments (e.g. 13C and 15N used simultaneously). See the Bioconductor package IsoCorrectoRGUI for a graphical user interface to IsoCorrectoR. NOTE: With R version 4.0.0, writing correction results to Excel files may currently not work on Windows. However, writing results to csv works as before.

r-illuminahumanv2-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/illuminaHumanv2.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina HumanWG6v2 annotation data (chip illuminaHumanv2)
Description:

Illumina HumanWG6v2 annotation data (chip illuminaHumanv2) assembled using data from public repositories.

r-illuminahumanmethylation450kprobe 2.0.6
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/IlluminaHumanMethylation450kprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type IlluminaHumanMethylation450k
Description:

Probe sequences from Illumina (ftp.illumina.com) for hm450 probes.

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-ibmq 1.50.0
Dependencies: gsl@2.8
Propagated dependencies: r-ggplot2@4.0.1 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: http://www.rglab.org
Licenses: Artistic License 2.0
Build system: r
Synopsis: integrated Bayesian Modeling of eQTL data
Description:

integrated Bayesian Modeling of eQTL data.

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-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-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-isee 2.22.0
Propagated dependencies: r-viridislite@0.4.2 r-vipor@0.4.7 r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-shinywidgets@0.9.0 r-shinyjs@2.1.0 r-shinydashboard@0.7.3 r-shinyace@0.4.4 r-shiny@1.11.1 r-s4vectors@0.48.0 r-rintrojs@0.3.4 r-mgcv@1.9-4 r-listviewer@4.0.0 r-igraph@2.2.1 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-dt@0.34.0 r-complexheatmap@2.26.0 r-colourpicker@1.3.0 r-circlize@0.4.16 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://isee.github.io/iSEE/
Licenses: Expat
Build system: r
Synopsis: Interactive SummarizedExperiment Explorer
Description:

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

r-isanalytics 1.20.1
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://calabrialab.github.io/ISAnalytics
Licenses: FSDG-compatible
Build system: r
Synopsis: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies
Description:

In gene therapy, stem cells are modified using viral vectors to deliver the therapeutic transgene and replace functional properties since the genetic modification is stable and inherited in all cell progeny. The retrieval and mapping of the sequences flanking the virus-host DNA junctions allows the identification of insertion sites (IS), essential for monitoring the evolution of genetically modified cells in vivo. A comprehensive toolkit for the analysis of IS is required to foster clonal trackign studies and supporting the assessment of safety and long term efficacy in vivo. This package is aimed at (1) supporting automation of IS workflow, (2) performing base and advance analysis for IS tracking (clonal abundance, clonal expansions and statistics for insertional mutagenesis, etc.), (3) providing basic biology insights of transduced stem cells in vivo.

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-interaccircos 1.20.0
Propagated dependencies: r-rcolorbrewer@1.1-3 r-plyr@1.8.9 r-htmlwidgets@1.6.4
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/interacCircos
Licenses: GPL 3
Build system: r
Synopsis: The Generation of Interactive Circos Plot
Description:

Implement in an efficient approach to display the genomic data, relationship, information in an interactive circular genome(Circos) plot. interacCircos are inspired by circosJS', BioCircos.js and NG-Circos and we integrate the modules of circosJS', BioCircos.js and NG-Circos into this R package, based on htmlwidgets framework.

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-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-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-icheck 1.40.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/iCheck
Licenses: GPL 2+
Build system: r
Synopsis: QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
Description:

QC pipeline and data analysis tools for high-dimensional Illumina mRNA expression data.

r-ivas 2.30.0
Propagated dependencies: r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-matrix@1.7-4 r-lme4@1.1-37 r-iranges@2.44.0 r-ggplot2@4.0.1 r-ggfortify@0.4.19 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-foreach@1.5.2 r-doparallel@1.0.17 r-biocparallel@1.44.0 r-biocgenerics@0.56.0 r-biobase@2.70.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/IVAS
Licenses: GPL 2
Build system: r
Synopsis: Identification of genetic Variants affecting Alternative Splicing
Description:

Identification of genetic variants affecting alternative splicing.

r-illuminahumanwgdaslv3-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/illuminaHumanWGDASLv3.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina HumanHT12WGDASLv3 annotation data (chip illuminaHumanWGDASLv3)
Description:

Illumina HumanHT12WGDASLv3 annotation data (chip illuminaHumanWGDASLv3) assembled using data from public repositories.

r-iterativebma 1.68.0
Propagated dependencies: r-leaps@3.2 r-bma@3.18.20 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: http://faculty.washington.edu/kayee/research.html
Licenses: GPL 2+
Build system: r
Synopsis: The Iterative Bayesian Model Averaging (BMA) algorithm
Description:

The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402).

r-indac-db 3.2.3
Propagated dependencies: r-org-dm-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/indac.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: INDAC FlyChip_long_oligonucleotide_002 (FL002) annotation data (chip indac)
Description:

INDAC FlyChip_long_oligonucleotide_002 (FL002) annotation data (chip indac) assembled using data from public repositories.

r-iterativebmasurv 1.68.0
Propagated dependencies: r-survival@3.8-3 r-leaps@3.2 r-bma@3.18.20
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: http://expression.washington.edu/ibmasurv/protected
Licenses: GPL 2+
Build system: r
Synopsis: The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis
Description:

The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data.

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-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.

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Total results: 69112