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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 search send a patch to ~whereiseveryone/toys@lists.sr.ht adding your channel as an entry in channels.scm.


r-tinesath1probe 1.50.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/tinesath1probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type tinesath1
Description:

This package was automatically created by package matchprobes version 1.4.0. The probe sequence data was obtained from http://www.affymetrix.com.

r-tidybulk 2.2.0
Propagated dependencies: r-ttservice@0.5.3 r-tidyselect@1.2.1 r-tidyr@1.3.2 r-tibble@3.3.1 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-rlang@1.1.7 r-purrr@1.2.1 r-matrix@1.7-4 r-magrittr@2.0.4 r-lifecycle@1.0.5 r-ggplot2@4.0.2 r-genomicranges@1.62.1 r-dplyr@1.2.0 r-crayon@1.5.3
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/stemangiola/tidybulk
Licenses: GPL 3
Build system: r
Synopsis: Brings transcriptomics to the tidyverse
Description:

This is a collection of utility functions that allow to perform exploration of and calculations to RNA sequencing data, in a modular, pipe-friendly and tidy fashion.

r-timecourse 1.84.0
Propagated dependencies: r-mass@7.3-65 r-marray@1.88.0 r-limma@3.66.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: http://www.bioconductor.org
Licenses: LGPL 2.0+
Build system: r
Synopsis: Statistical Analysis for Developmental Microarray Time Course Data
Description:

This package provides functions for data analysis and graphical displays for developmental microarray time course data.

r-trident 1.4.0
Propagated dependencies: r-tidyr@1.3.2 r-stringr@1.6.0 r-roll@1.2.1 r-patchwork@1.3.2 r-ggplot2@4.0.2 r-dplyr@1.2.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/jlmaier12/TrIdent
Licenses: GPL 2
Build system: r
Synopsis: TrIdent - Transduction Identification
Description:

The `TrIdent` R package automates the analysis of transductomics data by detecting, classifying, and characterizing read coverage patterns associated with potential transduction events. Transductomics is a DNA sequencing-based method for the detection and characterization of transduction events in pure cultures and complex communities. Transductomics relies on mapping sequencing reads from a viral-like particle (VLP)-fraction of a sample to contigs assembled from the metagenome (whole-community) of the same sample. Reads from bacterial DNA carried by VLPs will map back to the bacterial contigs of origin creating read coverage patterns indicative of ongoing transduction.

r-tenxvisiumdata 1.20.0
Propagated dependencies: r-spatialexperiment@1.20.0 r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/helenalc/TENxVisiumData
Licenses: Expat
Build system: r
Synopsis: Visium spatial gene expression data by 10X Genomics
Description:

Collection of Visium spatial gene expression datasets by 10X Genomics, formatted into objects of class SpatialExperiment. Data cover various organisms and tissues, and include: single- and multi-section experiments, as well as single sections subjected to both whole transcriptome and targeted panel analysis. Datasets may be used for testing of and as examples in packages, for tutorials and workflow demonstrations, or similar purposes.

r-tenxbraindata 1.32.0
Propagated dependencies: r-singlecellexperiment@1.32.0 r-hdf5array@1.38.0 r-experimenthub@3.0.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TENxBrainData
Licenses: FSDG-compatible
Build system: r
Synopsis: Data from the 10X 1.3 Million Brain Cell Study
Description:

Single-cell RNA-seq data for 1.3 million brain cells from E18 mice, generated by 10X Genomics.

r-tcgaworkflowdata 1.36.0
Propagated dependencies: r-summarizedexperiment@1.40.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://f1000research.com/articles/5-1542/v2
Licenses: GPL 3
Build system: r
Synopsis: Data for TCGA Workflow
Description:

This experimental data package contains 11 data sets necessary to follow the "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages".

r-tomatocdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/tomatocdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: tomatocdf
Description:

This package provides a package containing an environment representing the Tomato.cdf file.

r-txdb-athaliana-biomart-plantsmart25 3.1.3
Propagated dependencies: r-genomicfeatures@1.62.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TxDb.Athaliana.BioMart.plantsmart25
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for TxDb object(s)
Description:

Exposes an annotation databases generated from BioMart by exposing these as TxDb objects.

r-triplex 1.52.0
Propagated dependencies: r-xvector@0.50.0 r-s4vectors@0.48.0 r-iranges@2.44.0 r-genomicranges@1.62.1 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: http://www.fi.muni.cz/~lexa/triplex/
Licenses: FreeBSD
Build system: r
Synopsis: Search and visualize intramolecular triplex-forming sequences in DNA
Description:

This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.

r-txdb-ggallus-ucsc-galgal5-refgene 3.12.0
Propagated dependencies: r-genomicfeatures@1.62.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TxDb.Ggallus.UCSC.galGal5.refGene
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for TxDb object(s)
Description:

Exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

r-tidyprint 1.0.0
Propagated dependencies: r-vctrs@0.7.1 r-tidyr@1.3.2 r-tibble@3.3.1 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-s4vectors@0.48.0 r-rlang@1.1.7 r-purrr@1.2.1 r-pkgconfig@2.0.3 r-pillar@1.11.1 r-magrittr@2.0.4 r-fansi@1.0.7 r-dplyr@1.2.0 r-cli@3.6.5
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/tidyomics/tidyprint
Licenses: GPL 3
Build system: r
Synopsis: Custom Print Methods for SummarizedExperiment
Description:

This package provides customized print methods for SummarizedExperiment objects to enhance readability and usability within a tidy workflow. It offers consistent, tidyverse-aligned console displays, including alternative tibble abstractions for large genomic data to improve discoverability and interpretation. The package also includes unified, contextual messaging utilities intended for the tidyomics ecosystem.

r-transite 1.30.0
Propagated dependencies: r-tfmpvalue@1.0.0 r-stringr@1.6.0 r-scales@1.4.0 r-rcpp@1.1.1 r-gridextra@2.3 r-ggplot2@4.0.2 r-genomicranges@1.62.1 r-dplyr@1.2.0 r-biostrings@2.78.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://transite.mit.edu
Licenses: Expat
Build system: r
Synopsis: RNA-binding protein motif analysis
Description:

transite is a computational method that allows comprehensive analysis of the regulatory role of RNA-binding proteins in various cellular processes by leveraging preexisting gene expression data and current knowledge of binding preferences of RNA-binding proteins.

r-terratcgadata 1.16.0
Propagated dependencies: r-tidyr@1.3.2 r-tcgautils@1.30.2 r-s4vectors@0.48.0 r-readr@2.2.0 r-raggedexperiment@1.34.0 r-multiassayexperiment@1.36.1 r-genomicranges@1.62.1 r-dplyr@1.2.0 r-biocfilecache@3.0.0 r-anvilgcp@1.4.1 r-anvil@1.22.5
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/waldronlab/terraTCGAdata
Licenses: Artistic License 2.0
Build system: r
Synopsis: OpenAccess TCGA Data on Terra as MultiAssayExperiment
Description:

Leverage the existing open access TCGA data on Terra with well-established Bioconductor infrastructure. Make use of the Terra data model without learning its complexities. With a few functions, you can copy / download and generate a MultiAssayExperiment from the TCGA example workspaces provided by Terra.

r-tofsimsdata 1.40.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/tofsimsData
Licenses: GPL 3
Build system: r
Synopsis: Import, process and analysis of ToF-SIMS imaging data
Description:

This packages contains data to be used with the tofsims package.

r-txdb-sscrofa-ucsc-susscr3-refgene 3.12.0
Propagated dependencies: r-genomicfeatures@1.62.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TxDb.Sscrofa.UCSC.susScr3.refGene
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for TxDb object(s)
Description:

Exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

r-tmsig 1.6.0
Propagated dependencies: r-matrix@1.7-4 r-limma@3.66.0 r-gseabase@1.72.0 r-data-table@1.18.2.1 r-complexheatmap@2.26.1 r-circlize@0.4.17
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/EMSL-Computing/TMSig
Licenses: GPL 3+
Build system: r
Synopsis: Tools for Molecular Signatures
Description:

The TMSig package contains tools to prepare, analyze, and visualize named lists of sets, with an emphasis on molecular signatures (such as gene or kinase sets). It includes fast, memory efficient functions to construct sparse incidence and similarity matrices and filter, cluster, invert, and decompose sets. Additionally, bubble heatmaps can be created to visualize the results of any differential or molecular signatures analysis.

r-test3cdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/test3cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: test3cdf
Description:

This package provides a package containing an environment representing the Test3.CDF file.

r-tumourmethdata 1.9.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-rhdf5@2.54.1 r-r-utils@2.13.0 r-hdf5array@1.38.0 r-genomicranges@1.62.1 r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/richardheery/TumourMethData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Collection of DNA Methylation Datasets for Human Tumour Samples and Matching Normal Samples
Description:

TumourMethData collects tumour methylation data from a variety of different tumour types (and also matching normal samples where available) and produced with different technologies (e.g. WGBS, RRBS and methylation arrays) and provides them as RangedSummarizedExperiments. This facilitates easy extraction of methylation data for regions of interest across different tumour types and studies.

r-treeclimbr 1.8.0
Propagated dependencies: r-viridis@0.6.5 r-treesummarizedexperiment@2.18.0 r-tidyr@1.3.2 r-tibble@3.3.1 r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-rlang@1.1.7 r-ggtree@4.0.4 r-ggplot2@4.0.2 r-ggnewscale@0.5.2 r-edger@4.8.2 r-dplyr@1.2.0 r-dirmult@0.1.3-5 r-diffcyt@1.30.0 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/csoneson/treeclimbR
Licenses: Artistic License 2.0
Build system: r
Synopsis: An algorithm to find optimal signal levels in a tree
Description:

The arrangement of hypotheses in a hierarchical structure appears in many research fields and often indicates different resolutions at which data can be viewed. This raises the question of which resolution level the signal should best be interpreted on. treeclimbR provides a flexible method to select optimal resolution levels (potentially different levels in different parts of the tree), rather than cutting the tree at an arbitrary level. treeclimbR uses a tuning parameter to generate candidate resolutions and from these selects the optimal one.

r-topdownr 1.34.0
Propagated dependencies: r-s4vectors@0.48.0 r-psmatch@1.14.0 r-protgenerics@1.42.0 r-mzr@2.44.0 r-msnbase@2.36.0 r-matrix@1.7-4 r-ggplot2@4.0.2 r-biostrings@2.78.0 r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://codeberg.org/sgibb/topdownr/
Licenses: GPL 3+
Build system: r
Synopsis: Investigation of Fragmentation Conditions in Top-Down Proteomics
Description:

The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.

r-tidyspatialexperiment 1.8.0
Propagated dependencies: r-vctrs@0.7.1 r-ttservice@0.5.3 r-tidysinglecellexperiment@1.22.0 r-tidyselect@1.2.1 r-tidyr@1.3.2 r-tidygate@1.0.19 r-tibble@3.3.1 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-spatialexperiment@1.20.0 r-singlecellexperiment@1.32.0 r-shiny@1.11.1 r-s4vectors@0.48.0 r-rlang@1.1.7 r-purrr@1.2.1 r-plotly@4.12.0 r-pkgconfig@2.0.3 r-pillar@1.11.1 r-magick@2.9.1 r-lifecycle@1.0.5 r-ggplot2@4.0.2 r-fansi@1.0.7 r-dplyr@1.2.0 r-cli@3.6.5 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/william-hutchison/tidySpatialExperiment
Licenses: GPL 3+
Build system: r
Synopsis: SpatialExperiment with tidy principles
Description:

tidySpatialExperiment provides a bridge between the SpatialExperiment package and the tidyverse ecosystem. It creates an invisible layer that allows you to interact with a SpatialExperiment object as if it were a tibble; enabling the use of functions from dplyr, tidyr, ggplot2 and plotly. But, underneath, your data remains a SpatialExperiment object.

r-tidysbml 1.6.0
Propagated dependencies: r-xml2@1.5.2
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/veronicapaparozzi/tidysbml
Licenses: FSDG-compatible
Build system: r
Synopsis: Extract SBML's data into dataframes
Description:

Starting from one SBML file, it extracts information from each listOfCompartments, listOfSpecies and listOfReactions element by saving them into data frames. Each table provides one row for each entity (i.e. either compartment, species, reaction or speciesReference) and one set of columns for the attributes, one column for the content of the notes subelement and one set of columns for the content of the annotation subelement.

r-txdb-cfamiliaris-ucsc-canfam4-refgene 3.14.0
Propagated dependencies: r-genomicfeatures@1.62.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TxDb.Cfamiliaris.UCSC.canFam4.refGene
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for TxDb object(s)
Description:

Exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

Total packages: 3017