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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-tenet 1.4.0
Propagated dependencies: r-tenet-experimenthub@1.4.0 r-tcgabiolinks@2.40.0 r-survminer@0.5.2 r-survival@3.8-6 r-summarizedexperiment@1.42.0 r-sesamedata@1.30.0 r-sesame@1.30.0 r-seqlogo@1.78.0 r-s4vectors@0.50.1 r-rtracklayer@1.72.0 r-rcircos@1.2.2 r-r-utils@2.13.0 r-pastecs@1.4.2 r-multiassayexperiment@1.38.0 r-motifdb@1.54.0 r-matlab@1.0.4.1 r-iranges@2.46.0 r-ggplot2@4.0.3 r-genomicranges@1.64.0 r-experimenthub@3.2.0 r-bsgenome-hsapiens-ucsc-hg38@1.4.5 r-biostrings@2.80.1 r-bammtools@2.1.12 r-annotationhub@4.2.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/rhielab/TENET
Licenses: GPL 2
Build system: r
Synopsis: R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key transcription factors
Description:

TENET identifies key transcription factors (TFs) and regulatory elements (REs) linked to a specific cell type by finding significantly correlated differences in gene expression and RE DNA methylation between case and control input datasets, and identifying the top genes by number of significant RE DNA methylation site links. It also includes many tools for visualization and analysis of the results, including plots displaying and comparing methylation and expression data and methylation site link counts, survival analysis, TF motif searching in the vicinity of linked RE DNA methylation sites, custom TAD and peak overlap analysis, and UCSC Genome Browser track file generation. A utility function is also provided to download methylation, expression, and patient survival data from The Cancer Genome Atlas (TCGA) for use in TENET or other analyses.

r-target 1.26.0
Propagated dependencies: r-shiny@1.13.0 r-matrixstats@1.5.0 r-iranges@2.46.0 r-genomicranges@1.64.0 r-biocgenerics@0.58.1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/MahShaaban/target
Licenses: GPL 3
Build system: r
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-tcgacrcmrna 1.32.0
Propagated dependencies: r-biobase@2.72.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TCGAcrcmRNA
Licenses: GPL 2
Build system: r
Synopsis: TCGA CRC 450 mRNA dataset
Description:

colorectal cancer mRNA profile provided by TCGA.

r-txdb-hsapiens-ucsc-hg19-refgene 3.22.0
Propagated dependencies: r-genomicfeatures@1.64.0 r-annotationdbi@1.74.0
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
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-tfea-chip 1.32.0
Propagated dependencies: r-rlang@1.2.0 r-r-utils@2.13.0 r-org-mm-eg-db@3.23.0 r-org-hs-eg-db@3.23.1 r-iranges@2.46.0 r-genomicranges@1.64.0 r-genomicfeatures@1.64.0 r-experimenthub@3.2.0 r-dplyr@1.2.1 r-biomart@2.68.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/yberda/TFEA.ChIP
Licenses: Artistic License 2.0
Build system: r
Synopsis: TFEA.ChIP, a Tool Kit for Transcription Factor Enrichment
Description:

Package to analyze transcription factor enrichment in a gene set using data from ChIP-Seq experiments.

r-txdb-scerevisiae-ucsc-saccer2-sgdgene 3.2.2
Propagated dependencies: r-genomicfeatures@1.64.0 r-annotationdbi@1.74.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene
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@0.7.3 r-tidyr@1.3.2 r-tibble@3.3.1 r-summarizedexperiment@1.42.0 r-stringr@1.6.0 r-s4vectors@0.50.1 r-rlang@1.2.0 r-purrr@1.2.2 r-pkgconfig@2.0.3 r-pillar@1.11.1 r-magrittr@2.0.5 r-fansi@1.0.7 r-dplyr@1.2.1 r-cli@3.6.6
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-tapseq 1.24.0
Dependencies: blast+@2.17.0
Propagated dependencies: r-tidyr@1.3.2 r-s4vectors@0.50.1 r-iranges@2.46.0 r-genomicranges@1.64.0 r-genomicfeatures@1.64.0 r-genomicalignments@1.48.0 r-genomeinfodb@1.48.0 r-dplyr@1.2.1 r-bsgenome@1.80.0 r-biostrings@2.80.1 r-biocparallel@1.46.0 r-biocgenerics@0.58.1
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-tcseq 1.36.0
Propagated dependencies: r-summarizedexperiment@1.42.0 r-rsamtools@2.28.0 r-reshape2@1.4.5 r-locfit@1.5-9.12 r-iranges@2.46.0 r-ggplot2@4.0.3 r-genomicranges@1.64.0 r-genomicalignments@1.48.0 r-edger@4.10.0 r-e1071@1.7-17 r-cluster@2.1.8.2 r-biocgenerics@0.58.1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TCseq
Licenses: GPL 2+
Build system: r
Synopsis: Time course sequencing data analysis
Description:

Quantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of the temporal patterns of time course data.

r-tartare 1.26.0
Propagated dependencies: r-experimenthub@3.2.0 r-annotationhub@4.2.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/cpanse/tartare
Licenses: GPL 3
Build system: r
Synopsis: Raw ground spectra recorded on Thermo Fisher Scientific mass spectrometers
Description:

This package provides raw files recorded on different Liquid Chromatography Mass Spectrometry (LC-MS) instruments. All included MS instruments are manufactured by Thermo Fisher Scientific and belong to the Orbitrap Tribrid or Q Exactive Orbitrap family of instruments. Despite their common origin and shared hardware components, e.g., Orbitrap mass analyser, the above instruments tend to write data in different "dialects" in a shared binary file format (.raw). The intention behind tartare is to provide complex but slim real-world files that can be used to make code robust with respect to this diversity. In other words, it is intended for enhanced unit testing. The package is considered to be used with the rawrr package and the Spectra MsBackends.

r-tronco 2.44.0
Propagated dependencies: r-xtable@1.8-8 r-scales@1.4.0 r-rgraphviz@2.56.0 r-rcolorbrewer@1.1-3 r-r-matlab@3.7.0 r-iterators@1.0.14 r-igraph@2.3.1 r-gtools@3.9.5 r-gtable@0.3.6 r-gridextra@2.3 r-foreach@1.5.2 r-doparallel@1.0.17 r-circlize@0.4.18 r-bnlearn@5.1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://sites.google.com/site/troncopackage/
Licenses: GPL 3
Build system: r
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-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@4.0.3 r-dplyr@1.2.1
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-tcgaworkflowdata 1.36.0
Propagated dependencies: r-summarizedexperiment@1.42.0
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-tloh 1.19.0
Propagated dependencies: r-variantannotation@1.58.0 r-stringr@1.6.0 r-scales@1.4.0 r-purrr@1.2.2 r-naniar@1.1.0 r-matrixgenerics@1.24.0 r-ggplot2@4.0.3 r-genomicranges@1.64.0 r-dplyr@1.2.1 r-depmixs4@1.5-1 r-data-table@1.18.4 r-bestnormalize@1.9.2
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/USCDTG/tLOH
Licenses: Expat
Build system: r
Synopsis: Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations
Description:

tLOH, or transcriptomicsLOH, assesses evidence for loss of heterozygosity (LOH) in pre-processed spatial transcriptomics data. This tool requires spatial transcriptomics cluster and allele count information at likely heterozygous single-nucleotide polymorphism (SNP) positions in VCF format. Bayes factors are calculated at each SNP to determine likelihood of potential loss of heterozygosity event. Two plotting functions are included to visualize allele fraction and aggregated Bayes factor per chromosome. Data generated with the 10X Genomics Visium Spatial Gene Expression platform must be pre-processed to obtain an individual sample VCF with columns for each cluster. Required fields are allele depth (AD) with counts for reference/alternative alleles and read depth (DP).

r-toppgene 1.0.1
Propagated dependencies: r-yaml@2.3.12 r-xml2@1.5.2 r-s4vectors@0.50.1 r-readr@2.2.0 r-purrr@1.2.2 r-jsonlite@2.0.0 r-iranges@2.46.0 r-httr2@1.2.2 r-biocfilecache@3.2.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/ImmuSystems-lab/toppgene
Licenses: GPL 3+
Build system: r
Synopsis: Gene List Enrichment Analysis using the ToppGene Suite
Description:

The ToppGene Suite is a one-stop portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network. Although the ToppCluster web application provides convenient graphical access to the ToppGene Suite, the OpenAPI 3.0 compliant interface of ToppGene is better suited for automation and reproducibility. This package includes Bioconductor class interfaces and biological examples.

r-tfutils 1.32.0
Propagated dependencies: r-summarizedexperiment@1.42.0 r-shiny@1.13.0 r-rsamtools@2.28.0 r-rjson@0.2.23 r-readxl@1.5.0 r-org-hs-eg-db@3.23.1 r-miniui@0.1.2 r-magrittr@2.0.5 r-httr@1.4.8 r-gseabase@1.74.0 r-genomicfiles@1.48.0 r-dt@0.34.0 r-dplyr@1.2.1 r-biocfilecache@3.2.0 r-annotationdbi@1.74.0
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-tanggle 1.18.0
Propagated dependencies: r-rlang@1.2.0 r-phangorn@2.12.1 r-ggtree@4.2.0 r-ggplot2@4.0.3 r-dplyr@1.2.1 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://klausvigo.github.io/tanggle/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Visualization of Phylogenetic Networks
Description:

Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. ggtree and using functions from ape and phangorn'. It extends the ggtree package [@Yu2017] to allow the visualization of phylogenetic networks using the ggplot2 syntax. It offers an alternative to the plot functions already available in ape Paradis and Schliep (2019) <doi:10.1093/bioinformatics/bty633> and phangorn Schliep (2011) <doi:10.1093/bioinformatics/btq706>.

r-tissueenrich 1.32.0
Propagated dependencies: r-tidyr@1.3.2 r-summarizedexperiment@1.42.0 r-gseabase@1.74.0 r-ggplot2@4.0.3 r-dplyr@1.2.1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TissueEnrich
Licenses: Expat
Build system: r
Synopsis: Tissue-specific gene enrichment analysis
Description:

The TissueEnrich package is used to calculate enrichment of tissue-specific genes in a set of input genes. For example, the user can input the most highly expressed genes from RNA-Seq data, or gene co-expression modules to determine which tissue-specific genes are enriched in those datasets. Tissue-specific genes were defined by processing RNA-Seq data from the Human Protein Atlas (HPA) (Uhlén et al. 2015), GTEx (Ardlie et al. 2015), and mouse ENCODE (Shen et al. 2012) using the algorithm from the HPA (Uhlén et al. 2015).The hypergeometric test is being used to determine if the tissue-specific genes are enriched among the input genes. Along with tissue-specific gene enrichment, the TissueEnrich package can also be used to define tissue-specific genes from expression datasets provided by the user, which can then be used to calculate tissue-specific gene enrichments.

r-txdb-celegans-ucsc-ce11-refgene 3.4.6
Propagated dependencies: r-genomicfeatures@1.64.0 r-annotationdbi@1.74.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce11.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-trio 3.50.0
Propagated dependencies: r-survival@3.8-6 r-siggenes@1.86.0 r-logicreg@1.6.6 r-data-table@1.18.4
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/trio
Licenses: LGPL 2.0
Build system: r
Synopsis: Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
Description:

Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.

r-tmexplorer 1.22.0
Propagated dependencies: r-singlecellexperiment@1.34.0 r-matrix@1.7-5 r-biocfilecache@3.2.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TMExplorer
Licenses: Artistic License 2.0
Build system: r
Synopsis: Collection of Tumour Microenvironment Single-cell RNA Sequencing Datasets and Corresponding Metadata
Description:

This package provides a tool to search and download a collection of tumour microenvironment single-cell RNA sequencing datasets and their metadata. TMExplorer aims to act as a single point of entry for users looking to study the tumour microenvironment at the single cell level. Users can quickly search available datasets using the metadata table and then download the ones they are interested in for analysis.

r-teqc 4.34.0
Propagated dependencies: r-seqinfo@1.2.0 r-s4vectors@0.50.1 r-rsamtools@2.28.0 r-iranges@2.46.0 r-hwriter@1.3.2.1 r-genomicranges@1.64.0 r-biocgenerics@0.58.1 r-biobase@2.72.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TEQC
Licenses: GPL 2+
Build system: r
Synopsis: Quality control for target capture experiments
Description:

Target capture experiments combine hybridization-based (in solution or on microarrays) capture and enrichment of genomic regions of interest (e.g. the exome) with high throughput sequencing of the captured DNA fragments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.

r-tenxpbmcdata 1.30.0
Propagated dependencies: r-singlecellexperiment@1.34.0 r-hdf5array@1.40.0 r-experimenthub@3.2.0 r-annotationhub@4.2.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TENxPBMCData
Licenses: FSDG-compatible
Build system: r
Synopsis: PBMC data from 10X Genomics
Description:

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

Total packages: 3017