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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-icheck 1.40.0
Propagated dependencies: r-scatterplot3d@0.3-44 r-rgl@1.3.31 r-randomforest@4.7-1.2 r-preprocesscore@1.72.0 r-mass@7.3-65 r-lumi@2.62.0 r-lmtest@0.9-40 r-limma@3.66.0 r-gplots@3.2.0 r-geneselectmmd@2.54.0 r-biobase@2.70.0 r-affy@1.88.0
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-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-inpower 1.46.0
Propagated dependencies: r-mvtnorm@1.3-3
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/INPower
Licenses: FSDG-compatible
Build system: r
Synopsis: An R package for computing the number of susceptibility SNPs
Description:

An R package for computing the number of susceptibility SNPs and power of future studies.

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-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-illuminahumanv4-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/illuminaHumanv4.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina HumanHT12v4 annotation data (chip illuminaHumanv4)
Description:

Illumina HumanHT12v4 annotation data (chip illuminaHumanv4) assembled using data from public repositories.

r-igc 1.40.0
Propagated dependencies: r-plyr@1.8.9 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: http://github.com/ccwang002/iGC
Licenses: GPL 2
Build system: r
Synopsis: An integrated analysis package of Gene expression and Copy number alteration
Description:

This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data.

r-imcrtools 1.16.0
Propagated dependencies: r-vroom@1.6.6 r-viridis@0.6.5 r-tidyselect@1.2.1 r-tidygraph@1.3.1 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-spatialexperiment@1.20.0 r-singlecellexperiment@1.32.0 r-sf@1.0-23 r-scuttle@1.20.0 r-s4vectors@0.48.0 r-rtriangle@1.6-0.15 r-rlang@1.1.6 r-readr@2.1.6 r-pheatmap@1.0.13 r-matrixgenerics@1.22.0 r-magrittr@2.0.4 r-igraph@2.2.1 r-ggraph@2.2.2 r-ggplot2@4.0.1 r-ebimage@4.52.0 r-dt@0.34.0 r-dplyr@1.1.4 r-distances@0.1.13 r-data-table@1.17.8 r-cytomapper@1.22.0 r-concaveman@1.2.0 r-biocparallel@1.44.0 r-biocneighbors@2.4.0 r-abind@1.4-8
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.

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-iloreg 1.20.0
Propagated dependencies: r-umap@0.2.10.0 r-summarizedexperiment@1.40.0 r-sparsem@1.84-2 r-singlecellexperiment@1.32.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-rtsne@0.17 r-rspectra@0.16-2 r-reshape2@1.4.5 r-plyr@1.8.9 r-pheatmap@1.0.13 r-paralleldist@0.2.7 r-matrix@1.7-4 r-liblinear@2.10-24 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-dorng@1.8.6.2 r-desctools@0.99.60 r-dendextend@1.19.1 r-cowplot@1.2.0 r-cluster@2.1.8.1 r-aricode@1.0.3
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/elolab/ILoReg
Licenses: GPL 3
Build system: r
Synopsis: ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data
Description:

ILoReg is a tool for identification of cell populations from scRNA-seq data. In particular, ILoReg is useful for finding cell populations with subtle transcriptomic differences. The method utilizes a self-supervised learning method, called Iteratitive Clustering Projection (ICP), to find cluster probabilities, which are used in noise reduction prior to PCA and the subsequent hierarchical clustering and t-SNE steps. Additionally, functions for differential expression analysis to find gene markers for the populations and gene expression visualization are provided.

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-iyer517 1.52.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/Iyer517
Licenses: Artistic License 2.0
Build system: r
Synopsis: exprSets for Iyer, Eisen et all 1999 Science paper
Description:

representation of public Iyer data from http://genome-www.stanford.edu/serum/clusters.html.

r-islify 1.2.0
Propagated dependencies: r-tiff@0.1-12 r-rbioformats@1.10.0 r-png@0.1-8 r-matrix@1.7-4 r-dbscan@1.2.3 r-autothresholdr@1.4.3 r-abind@1.4-8
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/Bioconductor/islify
Licenses: GPL 3
Build system: r
Synopsis: Automatic scoring and classification of cell-based assay images
Description:

This software is meant to be used for classification of images of cell-based assays for neuronal surface autoantibody detection or similar techniques. It takes imaging files as input and creates a composite score from these, that for example can be used to classify samples as negative or positive for a certain antibody-specificity. The reason for its name is that I during its creation have thought about the individual picture as an archielago where we with different filters control the water level as well as ground characteristica, thereby finding islands of interest.

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-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-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-iseede 1.8.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-shiny@1.11.1 r-s4vectors@0.48.0 r-isee@2.22.0 r-edger@4.8.0 r-deseq2@1.50.2
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/iSEE/iSEEde
Licenses: Artistic License 2.0
Build system: r
Synopsis: iSEE extension for panels related to differential expression 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 differential expression results. This package does not perform differential expression. Instead, it provides methods to embed precomputed differential expression results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.

r-isanalytics 1.20.1
Propagated dependencies: r-vegan@2.7-2 r-tidyr@1.3.1 r-tibble@3.3.0 r-stringr@1.6.0 r-shinywidgets@0.9.0 r-shiny@1.11.1 r-rlang@1.1.6 r-readxl@1.4.5 r-readr@2.1.6 r-purrr@1.2.0 r-lubridate@1.9.4 r-lifecycle@1.0.4 r-glue@1.8.0 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-fs@1.6.6 r-forcats@1.0.1 r-dt@0.34.0 r-dplyr@1.1.4 r-datamods@1.5.3 r-data-table@1.17.8 r-bslib@0.9.0
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-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-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-icare 1.38.0
Propagated dependencies: r-plotrix@3.8-13 r-hmisc@5.2-4 r-gtools@3.9.5
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/iCARE
Licenses: FSDG-compatible
Build system: r
Synopsis: Individualized Coherent Absolute Risk Estimation (iCARE)
Description:

An R package to build, validate and apply absolute risk models.

r-ibh 1.58.0
Propagated dependencies: r-simpintlists@1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/ibh
Licenses: GPL 2+
Build system: r
Synopsis: Interaction Based Homogeneity for Evaluating Gene Lists
Description:

This package contains methods for calculating Interaction Based Homogeneity to evaluate fitness of gene lists to an interaction network which is useful for evaluation of clustering results and gene list analysis. BioGRID interactions are used in the calculation. The user can also provide their own interactions.

r-ideal 2.4.0
Propagated dependencies: r-upsetr@1.4.0 r-topgo@2.62.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-shinydashboard@0.7.3 r-shinybs@0.61.1 r-shinyace@0.4.4 r-shiny@1.11.1 r-s4vectors@0.48.0 r-rmarkdown@2.30 r-rlang@1.1.6 r-rintrojs@0.3.4 r-rentrez@1.2.4 r-plotly@4.11.0 r-pheatmap@1.0.13 r-mosdef@1.6.0 r-limma@3.66.0 r-knitr@1.50 r-iranges@2.44.0 r-ihw@1.38.0 r-heatmaply@1.6.0 r-gplots@3.2.0 r-gostats@2.76.0 r-goseq@1.62.0 r-go-db@3.22.0 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-dt@0.34.0 r-dplyr@1.1.4 r-deseq2@1.50.2 r-biocparallel@1.44.0 r-base64enc@0.1-3 r-annotationdbi@1.72.0
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.

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