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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-tapseq 1.22.1
Dependencies: blast+@2.17.0
Propagated dependencies: r-tidyr@1.3.1 r-s4vectors@0.48.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomicalignments@1.46.0 r-genomeinfodb@1.46.0 r-dplyr@1.1.4 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/argschwind/TAPseq
Licenses: Expat
Build system: r
Synopsis: Targeted scRNA-seq primer design for TAP-seq
Description:

Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using Primer3. Potential off-targets can be estimated with BLAST. Requires working installations of Primer3 and BLASTn.

r-tumourmethdata 1.8.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-rhdf5@2.54.0 r-r-utils@2.13.0 r-hdf5array@1.38.0 r-genomicranges@1.62.0 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-txdb-mmusculus-ucsc-mm39-knowngene 3.22.0
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.Mmusculus.UCSC.mm39.knownGene
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-tenet-experimenthub 1.2.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-multiassayexperiment@1.36.1 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/rhielab/TENET.ExperimentHub
Licenses: GPL 2
Build system: r
Synopsis: Experiment data for the TENET package
Description:

ExperimentHub package containing datasets for use in the TENET package's vignette and function examples. These include a variety of different objects to illustrate different datasets used in TENET functions. Where applicable, all datasets are aligned to the hg38 human genome.

r-tfhaz 1.32.0
Propagated dependencies: r-s4vectors@0.48.0 r-orfik@1.30.2 r-iranges@2.44.0 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TFHAZ
Licenses: Artistic License 2.0
Build system: r
Synopsis: Transcription Factor High Accumulation Zones
Description:

It finds trascription factor (TF) high accumulation DNA zones, i.e., regions along the genome where there is a high presence of different transcription factors. Starting from a dataset containing the genomic positions of TF binding regions, for each base of the selected chromosome the accumulation of TFs is computed. Three different types of accumulation (TF, region and base accumulation) are available, together with the possibility of considering, in the single base accumulation computing, the TFs present not only in that single base, but also in its neighborhood, within a window of a given width. Two different methods for the search of TF high accumulation DNA zones, called "binding regions" and "overlaps", are available. In addition, some functions are provided in order to analyze, visualize and compare results obtained with different input parameters.

r-transomicsdata 1.6.0
Propagated dependencies: r-s4vectors@0.48.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/PYangLab/TransOmicsData
Licenses: FSDG-compatible
Build system: r
Synopsis: collection of trans-omics datasets across various biological systems
Description:

This package contains a collection of trans-omics datasets generated using various sequencing technologies such as RNA-seq, Mass spectrometry and ChIP-seq. Modalities include the bulk profiling of the phosphoproteome, proteome, transcriptome and epigenome. Data reflects the timecourses of different developmental systems from the mouse or human.

r-tidycoverage 1.6.0
Propagated dependencies: r-vctrs@0.6.5 r-tidyr@1.3.1 r-summarizedexperiment@1.40.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rlang@1.1.6 r-purrr@1.2.0 r-pillar@1.11.1 r-iranges@2.44.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-fansi@1.0.7 r-dplyr@1.1.4 r-cli@3.6.5 r-biocparallel@1.44.0 r-biocio@1.20.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/js2264/tidyCoverage
Licenses: Expat
Build system: r
Synopsis: Extract and aggregate genomic coverage over features of interest
Description:

`tidyCoverage` framework enables tidy manipulation of collections of genomic tracks and features using `tidySummarizedExperiment` methods. It facilitates the extraction, aggregation and visualization of genomic coverage over individual or thousands of genomic loci, relying on `CoverageExperiment` and `AggregatedCoverage` classes. This accelerates the integration of genomic track data in genomic analysis workflows.

r-tidybulk 2.0.1
Propagated dependencies: r-ttservice@0.5.3 r-tidyselect@1.2.1 r-tidyr@1.3.1 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-rlang@1.1.6 r-purrr@1.2.0 r-matrix@1.7-4 r-magrittr@2.0.4 r-lifecycle@1.0.4 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-dplyr@1.1.4 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-txdb-ptroglodytes-ucsc-pantro6-refgene 3.10.0
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.Ptroglodytes.UCSC.panTro6.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-tripr 1.16.0
Propagated dependencies: r-vegan@2.7-2 r-stringr@1.6.0 r-stringdist@0.9.15 r-shinyjs@2.1.0 r-shinyfiles@0.9.3 r-shinybs@0.61.1 r-shiny@1.11.1 r-rcolorbrewer@1.1-3 r-plyr@1.8.9 r-plotly@4.11.0 r-plot3d@1.4.2 r-gridextra@2.3 r-golem@0.5.1 r-dt@0.34.0 r-dplyr@1.1.4 r-data-table@1.17.8 r-config@0.3.2
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/BiodataAnalysisGroup/tripr
Licenses: Expat
Build system: r
Synopsis: T-cell Receptor/Immunoglobulin Profiler (TRIP)
Description:

TRIP is a software framework that provides analytics services on antigen receptor (B cell receptor immunoglobulin, BcR IG | T cell receptor, TR) gene sequence data. It is a web application written in R Shiny. It takes as input the output files of the IMGT/HighV-Quest tool. Users can select to analyze the data from each of the input samples separately, or the combined data files from all samples and visualize the results accordingly.

r-txdb-ggallus-ucsc-galgal6-refgene 3.10.0
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.galGal6.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-timecourse 1.82.0
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-tidysummarizedexperiment 1.20.1
Propagated dependencies: r-vctrs@0.6.5 r-ttservice@0.5.3 r-tidyselect@1.2.1 r-tidyr@1.3.1 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-s4vectors@0.48.0 r-rlang@1.1.6 r-purrr@1.2.0 r-plyxp@1.4.3 r-pkgconfig@2.0.3 r-pillar@1.11.1 r-magrittr@2.0.4 r-lifecycle@1.0.4 r-ggplot2@4.0.1 r-generics@0.1.4 r-fansi@1.0.7 r-ellipsis@0.3.2 r-dplyr@1.1.4 r-cli@3.6.5
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/stemangiola/tidySummarizedExperiment
Licenses: GPL 3
Build system: r
Synopsis: Brings SummarizedExperiment to the Tidyverse
Description:

The tidySummarizedExperiment package provides a set of tools for creating and manipulating tidy data representations of SummarizedExperiment objects. SummarizedExperiment is a widely used data structure in bioinformatics for storing high-throughput genomic data, such as gene expression or DNA sequencing data. The tidySummarizedExperiment package introduces a tidy framework for working with SummarizedExperiment objects. It allows users to convert their data into a tidy format, where each observation is a row and each variable is a column. This tidy representation simplifies data manipulation, integration with other tidyverse packages, and enables seamless integration with the broader ecosystem of tidy tools for data analysis.

r-txdb-drerio-ucsc-danrer10-refgene 3.4.6
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.Drerio.UCSC.danRer10.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-transomics2cytoscape 1.20.0
Propagated dependencies: r-tibble@3.3.0 r-rcy3@2.30.0 r-purrr@1.2.0 r-pbapply@1.7-4 r-keggrest@1.50.0 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/transomics2cytoscape
Licenses: Artistic License 2.0
Build system: r
Synopsis: tool set for 3D Trans-Omic network visualization with Cytoscape
Description:

transomics2cytoscape generates a file for 3D transomics visualization by providing input that specifies the IDs of multiple KEGG pathway layers, their corresponding Z-axis heights, and an input that represents the edges between the pathway layers. The edges are used, for example, to describe the relationships between kinase on a pathway and enzyme on another pathway. This package automates creation of a transomics network as shown in the figure in Yugi.2014 (https://doi.org/10.1016/j.celrep.2014.07.021) using Cytoscape automation (https://doi.org/10.1186/s13059-019-1758-4).

r-timeomics 1.22.0
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.3.0 r-stringr@1.6.0 r-purrr@1.2.0 r-plyr@1.8.9 r-mixomics@6.34.0 r-magrittr@2.0.4 r-lmtest@0.9-40 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-dplyr@1.1.4 r-checkmate@2.3.3
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/timeOmics
Licenses: GPL 3
Build system: r
Synopsis: Time-Course Multi-Omics data integration
Description:

timeOmics is a generic data-driven framework to integrate multi-Omics longitudinal data measured on the same biological samples and select key temporal features with strong associations within the same sample group. The main steps of timeOmics are: 1. Plaform and time-specific normalization and filtering steps; 2. Modelling each biological into one time expression profile; 3. Clustering features with the same expression profile over time; 4. Post-hoc validation step.

r-tfutils 1.30.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-shiny@1.11.1 r-rsamtools@2.26.0 r-rjson@0.2.23 r-readxl@1.4.5 r-org-hs-eg-db@3.22.0 r-miniui@0.1.2 r-magrittr@2.0.4 r-httr@1.4.7 r-gseabase@1.72.0 r-genomicfiles@1.46.0 r-dt@0.34.0 r-dplyr@1.1.4 r-biocfilecache@3.0.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TFutils
Licenses: Artistic License 2.0
Build system: r
Synopsis: TFutils
Description:

This package helps users to work with TF metadata from various sources. Significant catalogs of TFs and classifications thereof are made available. Tools for working with motif scans are also provided.

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-tidyflowcore 1.4.0
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.3.0 r-stringr@1.6.0 r-rlang@1.1.6 r-purrr@1.2.0 r-ggplot2@4.0.1 r-flowcore@2.22.0 r-dplyr@1.1.4 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/keyes-timothy/tidyFlowCore
Licenses: Expat
Build system: r
Synopsis: tidyFlowCore: Bringing flowCore to the tidyverse
Description:

tidyFlowCore bridges the gap between flow cytometry analysis using the flowCore Bioconductor package and the tidy data principles advocated by the tidyverse. It provides a suite of dplyr-, ggplot2-, and tidyr-like verbs specifically designed for working with flowFrame and flowSet objects as if they were tibbles; however, your data remain flowCore data structures under this layer of abstraction. tidyFlowCore enables intuitive and streamlined analysis workflows that can leverage both the Bioconductor and tidyverse ecosystems for cytometry data.

r-txdb-rnorvegicus-ucsc-rn5-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.Rnorvegicus.UCSC.rn5.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-tweedeseqcountdata 1.48.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/isglobal-brge/tweeDEseqCountData/
Licenses: Expat
Build system: r
Synopsis: RNA-seq count data employed in the vignette of the tweeDEseq package
Description:

RNA-seq count data from Pickrell et al. (2010) employed to illustrate the use of the Poisson-Tweedie family of distributions with the tweeDEseq package.

r-txdb-athaliana-biomart-plantsmart22 3.0.1
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.plantsmart22
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-treeandleaf 1.22.0
Propagated dependencies: r-reder@3.6.0 r-igraph@2.2.1 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TreeAndLeaf
Licenses: Artistic License 2.0
Build system: r
Synopsis: Displaying binary trees with focus on dendrogram leaves
Description:

The TreeAndLeaf package combines unrooted and force-directed graph algorithms in order to layout binary trees, aiming to represent multiple layers of information onto dendrogram leaves.

r-tcgamethylation450k 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TCGAMethylation450k
Licenses: GPL 2
Build system: r
Synopsis: The Cancer Genome Atlas Illumina 450k methylation example data
Description:

The Cancer Genome Atlas (TCGA) is applying genomics technologies to over 20 different types of cancer. This package contains a small set of 450k array data in idat format.

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