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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-tcgaworkflowdata 1.34.0
Propagated dependencies: r-summarizedexperiment@1.38.1
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
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-txdb-athaliana-biomart-plantsmart25 3.1.3
Propagated dependencies: r-genomicfeatures@1.60.0 r-annotationdbi@1.70.0
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
Synopsis: Annotation package for TxDb object(s)
Description:

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

r-tronco 2.42.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://sites.google.com/site/troncopackage/
Licenses: GPL 3
Synopsis: TRONCO, an R package for TRanslational ONCOlogy
Description:

The TRONCO (TRanslational ONCOlogy) R package collects algorithms to infer progression models via the approach of Suppes-Bayes Causal Network, both from an ensemble of tumors (cross-sectional samples) and within an individual patient (multi-region or single-cell samples). The package provides parallel implementation of algorithms that process binary matrices where each row represents a tumor sample and each column a single-nucleotide or a structural variant driving the progression; a 0/1 value models the absence/presence of that alteration in the sample. The tool can import data from plain, MAF or GISTIC format files, and can fetch it from the cBioPortal for cancer genomics. Functions for data manipulation and visualization are provided, as well as functions to import/export such data to other bioinformatics tools for, e.g, clustering or detection of mutually exclusive alterations. Inferred models can be visualized and tested for their confidence via bootstrap and cross-validation. TRONCO is used for the implementation of the Pipeline for Cancer Inference (PICNIC).

r-tidyspatialexperiment 1.6.2
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/william-hutchison/tidySpatialExperiment
Licenses: GPL 3+
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-tiledbarray 1.20.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/LTLA/TileDBArray
Licenses: Expat
Synopsis: Using TileDB as a DelayedArray Backend
Description:

This package implements a DelayedArray backend for reading and writing dense or sparse arrays in the TileDB format. The resulting TileDBArrays are compatible with all Bioconductor pipelines that can accept DelayedArray instances.

r-tbx20bamsubset 1.46.0
Propagated dependencies: r-xtable@1.8-4 r-rsamtools@2.24.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TBX20BamSubset
Licenses: LGPL 2.0+
Synopsis: Subset of BAM files from the "TBX20" experiment
Description:

Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. A subset of the RNA-Seq data.

r-tbsignatureprofiler 1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/wejlab/TBSignatureProfiler
Licenses: Expat
Synopsis: Profile RNA-Seq Data Using TB Pathway Signatures
Description:

Gene signatures of TB progression, TB disease, and other TB disease states have been validated and published previously. This package aggregates known signatures and provides computational tools to enlist their usage on other datasets. The TBSignatureProfiler makes it easy to profile RNA-Seq data using these signatures and includes common signature profiling tools including ASSIGN, GSVA, and ssGSEA. Original models for some gene signatures are also available. A shiny app provides some functionality alongside for detailed command line accessibility.

r-txdb-rnorvegicus-ucsc-rn7-refgene 3.15.0
Propagated dependencies: r-genomicfeatures@1.60.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TxDb.Rnorvegicus.UCSC.rn7.refGene
Licenses: Artistic License 2.0
Synopsis: Annotation package for TxDb object(s)
Description:

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

r-txdb-cfamiliaris-ucsc-canfam6-refgene 3.17.0
Propagated dependencies: r-genomicfeatures@1.60.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TxDb.Cfamiliaris.UCSC.canFam6.refGene
Licenses: Artistic License 2.0
Synopsis: Annotation package for TxDb object(s)
Description:

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

r-txdb-hsapiens-ucsc-hg19-refgene 3.22.0
Propagated dependencies: r-genomicfeatures@1.60.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.refGene
Licenses: Artistic License 2.0
Synopsis: Annotation package for TxDb object(s)
Description:

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

r-taxsea 1.2.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/feargalr/taxsea
Licenses: GPL 3
Synopsis: Taxon Set Enrichment Analysis
Description:

TaxSEA is an R package for Taxon Set Enrichment Analysis, which utilises a Kolmogorov-Smirnov test analyses to investigate differential abundance analysis output for whether there are alternations in a-priori defined sets of taxa from public databases (BugSigDB, MiMeDB, GutMGene, mBodyMap, BacDive and GMRepoV2) and collated from the literature. TaxSEA takes as input a list of taxonomic identifiers (e.g. species names, NCBI IDs etc.) and a rank (E.g. fold change, correlation coefficient). TaxSEA be applied to any microbiota taxonomic profiling technology (array-based, 16S rRNA gene sequencing, shotgun metagenomics & metatranscriptomics etc.) and enables researchers to rapidly contextualize their findings within the broader literature to accelerate interpretation of results.

r-tuberculosis 1.16.0
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.2.1 r-summarizedexperiment@1.38.1 r-stringr@1.5.1 r-s4vectors@0.46.0 r-rlang@1.1.6 r-purrr@1.0.4 r-magrittr@2.0.3 r-experimenthub@2.16.0 r-dplyr@1.1.4 r-annotationhub@3.16.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/schifferl/tuberculosis
Licenses: Artistic License 2.0
Synopsis: Tuberculosis Gene Expression Data for Machine Learning
Description:

The tuberculosis R/Bioconductor package features tuberculosis gene expression data for machine learning. All human samples from GEO that did not come from cell lines, were not taken postmortem, and did not feature recombination have been included. The package has more than 10,000 samples from both microarray and sequencing studies that have been processed from raw data through a hyper-standardized, reproducible pipeline.

r-tenxpbmcdata 1.28.0
Propagated dependencies: r-singlecellexperiment@1.30.1 r-hdf5array@1.36.0 r-experimenthub@2.16.0 r-annotationhub@3.16.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TENxPBMCData
Licenses: FSDG-compatible
Synopsis: PBMC data from 10X Genomics
Description:

Single-cell RNA-seq data for on PBMC cells, generated by 10X Genomics.

r-txdb-rnorvegicus-ucsc-rn6-ncbirefseq 3.12.0
Propagated dependencies: r-genomicfeatures@1.60.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq
Licenses: Artistic License 2.0
Synopsis: Annotation package for TxDb object(s)
Description:

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

r-timerquant 1.39.0
Propagated dependencies: r-shiny@1.10.0 r-locfit@1.5-9.12 r-gridextra@2.3 r-ggplot2@3.5.2 r-dplyr@1.1.4 r-desolve@1.40
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TimerQuant
Licenses: Artistic License 2.0
Synopsis: Timer Quantification
Description:

Supplementary Data package for tandem timer methods paper by Barry et al. (2015) including TimerQuant shiny applications.

r-targetsearch 2.12.0
Propagated dependencies: r-ncdf4@1.24 r-assertthat@0.2.1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/acinostroza/TargetSearch
Licenses: GPL 2+
Synopsis: package for the analysis of GC-MS metabolite profiling data
Description:

This packages provides a flexible, fast and accurate method for targeted pre-processing of GC-MS data. The user provides a (often very large) set of GC chromatograms and a metabolite library of targets. The package will automatically search those targets in the chromatograms resulting in a data matrix that can be used for further data analysis.

r-tidysinglecellexperiment 1.20.1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/stemangiola/tidySingleCellExperiment
Licenses: GPL 3
Synopsis: Brings SingleCellExperiment to the Tidyverse
Description:

tidySingleCellExperiment is an adapter that abstracts the SingleCellExperiment container in the form of a tibble'. This allows *tidy* data manipulation, nesting, and plotting. For example, a tidySingleCellExperiment is directly compatible with functions from tidyverse packages `dplyr` and `tidyr`, as well as plotting with `ggplot2` and `plotly`. In addition, the package provides various utility functions specific to single-cell omics data analysis (e.g., aggregation of cell-level data to pseudobulks).

r-turbonorm 1.58.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: http://www.humgen.nl/MicroarrayAnalysisGroup.html
Licenses: LGPL 2.0+
Synopsis: fast scatterplot smoother suitable for microarray normalization
Description:

This package provides a fast scatterplot smoother based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available.

r-tidybulk 2.0.1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/stemangiola/tidybulk
Licenses: GPL 3
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-targetscoredata 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TargetScoreData
Licenses: GPL 2
Synopsis: TargetScoreData
Description:

Precompiled and processed miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using the package TargetScore (download separately).

r-timecoursedata 1.20.0
Propagated dependencies: r-summarizedexperiment@1.38.1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/timecoursedata
Licenses: FSDG-compatible
Synopsis: data package for timecourse RNA-seq and microarray gene expression data sets
Description:

This data package contains timecourse gene expression data sets. The first dataset, from Shoemaker et al, consists of microarray samples from lung tissue of mice exposed to different influenzy strains from 14 timepoints. The two other datasets are leaf and root samples from sorghum crops exposed to pre- and post-flowering drought stress and a control condition, sampled across the plants lifetime.

r-top 1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/Harry25R/TOP
Licenses: GPL 3
Synopsis: TOP Constructs Transferable Model Across Gene Expression Platforms
Description:

TOP constructs a transferable model across gene expression platforms for prospective experiments. Such a transferable model can be trained to make predictions on independent validation data with an accuracy that is similar to a re-substituted model. The TOP procedure also has the flexibility to be adapted to suit the most common clinical response variables, including linear response, binomial and Cox PH models.

r-target 1.24.0
Propagated dependencies: r-shiny@1.10.0 r-matrixstats@1.5.0 r-iranges@2.42.0 r-genomicranges@1.60.0 r-biocgenerics@0.54.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/MahShaaban/target
Licenses: GPL 3
Synopsis: Predict Combined Function of Transcription Factors
Description:

Implement the BETA algorithm for infering direct target genes from DNA-binding and perturbation expression data Wang et al. (2013) <doi: 10.1038/nprot.2013.150>. Extend the algorithm to predict the combined function of two DNA-binding elements from comprable binding and expression data.

r-tabulamurisdata 1.28.0
Propagated dependencies: r-experimenthub@2.16.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TabulaMurisData
Licenses: Expat
Synopsis: 10x And SmartSeq2 Data From The Tabula Muris Consortium
Description:

Access to processed 10x (droplet) and SmartSeq2 (on FACS-sorted cells) single-cell RNA-seq data from the Tabula Muris consortium (http://tabula-muris.ds.czbiohub.org/).

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