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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-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-iscream 1.0.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://huishenlab.github.io/iscream/
Licenses: Expat
Build system: r
Synopsis: Make fast and memory efficient BED file queries, summaries and matrices
Description:

BED files store ranged genomic data that can be queried even when the files are compressed. iscream can query data from BED files and return them in muliple formats: parsed records or their summary statistics as data frames or GenomicRanges objects, and matrices as matrix, GenomicRanges, or SummarizedExperiment objects. iscream also provides specialized support for importing methylation data.

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-icetea 1.28.0
Propagated dependencies: r-variantannotation@1.56.0 r-txdb-dmelanogaster-ucsc-dm6-ensgene@3.12.0 r-summarizedexperiment@1.40.0 r-shortread@1.68.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rsamtools@2.26.0 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-genomicalignments@1.46.0 r-edger@4.8.0 r-deseq2@1.50.2 r-csaw@1.44.0 r-biostrings@2.78.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/vivekbhr/icetea
Licenses: FSDG-compatible
Build system: r
Synopsis: Integrating Cap Enrichment with Transcript Expression Analysis
Description:

icetea (Integrating Cap Enrichment with Transcript Expression Analysis) provides functions for end-to-end analysis of multiple 5'-profiling methods such as CAGE, RAMPAGE and MAPCap, beginning from raw reads to detection of transcription start sites using replicates. It also allows performing differential TSS detection between group of samples, therefore, integrating the mRNA cap enrichment information with transcript expression analysis.

r-illuminahumanv1-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/illuminaHumanv1.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina HumanWG6v1 annotation data (chip illuminaHumanv1)
Description:

Illumina HumanWG6v1 annotation data (chip illuminaHumanv1) assembled using data from public repositories.

r-illuminamousev2-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/illuminaMousev2.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina MouseWG6v2 annotation data (chip illuminaMousev2)
Description:

Illumina MouseWG6v2 annotation data (chip illuminaMousev2) assembled using data from public repositories.

r-imodmix 1.0.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/biodatalab/iModMix
Licenses: GPL 3
Build system: r
Synopsis: Integrative Modules for Multi-Omics Data
Description:

The iModMix network-based method offers an integrated framework for analyzing multi-omics data, including metabolomics, proteomics, and transcriptomics data, enabling the exploration of intricate molecular associations within heterogeneous biological systems.

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-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-informeasure 1.20.0
Propagated dependencies: r-entropy@1.3.2
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/chupan1218/Informeasure
Licenses: Artistic License 2.0
Build system: r
Synopsis: R implementation of information measures
Description:

This package consolidates a comprehensive set of information measurements, encompassing mutual information, conditional mutual information, interaction information, partial information decomposition, and part mutual information.

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-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-isobar 1.56.0
Propagated dependencies: r-plyr@1.8.9 r-ggplot2@4.0.1 r-distr@2.9.7 r-biomart@2.66.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/fbreitwieser/isobar
Licenses: LGPL 2.0
Build system: r
Synopsis: Analysis and quantitation of isobarically tagged MSMS proteomics data
Description:

isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. Features modules for integrating and validating PTM-centric datasets (isobar-PTM). More information on http://www.ms-isobar.org.

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-illuminamousev1-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/illuminaMousev1.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina MouseWG6v1 annotation data (chip illuminaMousev1)
Description:

Illumina MouseWG6v1 annotation data (chip illuminaMousev1) 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-iseehex 1.12.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-shiny@1.11.1 r-isee@2.22.0 r-hexbin@1.28.5 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://github.com/iSEE/iSEEhex
Licenses: Artistic License 2.0
Build system: r
Synopsis: iSEE extension for summarising data points in hexagonal bins
Description:

This package provides panels summarising data points in hexagonal bins for `iSEE`. It is part of `iSEEu`, the iSEE universe of panels that extend the `iSEE` package.

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-ipath 1.16.0
Channel: guix-bioc
Location: guix-bioc/packages/i.scm (guix-bioc packages i)
Home page: https://bioconductor.org/packages/iPath
Licenses: GPL 2
Build system: r
Synopsis: iPath pipeline for detecting perturbed pathways at individual level
Description:

iPath is the Bioconductor package used for calculating personalized pathway score and test the association with survival outcomes. Abundant single-gene biomarkers have been identified and used in the clinics. However, hundreds of oncogenes or tumor-suppressor genes are involved during the process of tumorigenesis. We believe individual-level expression patterns of pre-defined pathways or gene sets are better biomarkers than single genes. In this study, we devised a computational method named iPath to identify prognostic biomarker pathways, one sample at a time. To test its utility, we conducted a pan-cancer analysis across 14 cancer types from The Cancer Genome Atlas and demonstrated that iPath is capable of identifying highly predictive biomarkers for clinical outcomes, including overall survival, tumor subtypes, and tumor stage classifications. We found that pathway-based biomarkers are more robust and effective than single genes.

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-illuminahumanv3-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/illuminaHumanv3.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina HumanHT12v3 annotation data (chip illuminaHumanv3)
Description:

Illumina HumanHT12v3 annotation data (chip illuminaHumanv3) assembled using data from public repositories.

r-imagetcga 1.2.0
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-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-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.

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Total results: 69112