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/_/ /      / / /____\/ /       \ \_\\ \/___/ /
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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-target 1.24.0
Propagated dependencies: r-shiny@1.11.1 r-matrixstats@1.5.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-biocgenerics@0.56.0
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-tracktables 1.44.0
Propagated dependencies: r-xvector@0.50.0 r-xml@3.99-0.20 r-tractor-base@3.5.0 r-stringr@1.6.0 r-rsamtools@2.26.0 r-rcolorbrewer@1.1-3 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/tracktables
Licenses: GPL 3+
Build system: r
Synopsis: Build IGV tracks and HTML reports
Description:

This package provides methods to create complex IGV genome browser sessions and dynamic IGV reports in HTML pages.

r-txdb-scerevisiae-ucsc-saccer2-sgdgene 3.2.2
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.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-tomoseqr 1.14.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/tomoseqr
Licenses: Expat
Build system: r
Synopsis: R Package for Analyzing Tomo-seq Data
Description:

`tomoseqr` is an R package for analyzing Tomo-seq data. Tomo-seq is a genome-wide RNA tomography method that combines combining high-throughput RNA sequencing with cryosectioning for spatially resolved transcriptomics. `tomoseqr` reconstructs 3D expression patterns from tomo-seq data and visualizes the reconstructed 3D expression patterns.

r-tmixclust 1.32.0
Propagated dependencies: r-zoo@1.8-14 r-spem@1.50.0 r-mvtnorm@1.3-3 r-gss@2.2-10 r-flexclust@1.5.0 r-cluster@2.1.8.1 r-biocparallel@1.44.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TMixClust
Licenses: FSDG-compatible
Build system: r
Synopsis: Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines
Description:

Implementation of a clustering method for time series gene expression data based on mixed-effects models with Gaussian variables and non-parametric cubic splines estimation. The method can robustly account for the high levels of noise present in typical gene expression time series datasets.

r-tofsimsdata 1.38.0
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-tigre 1.64.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/ahonkela/tigre
Licenses: AGPL 3
Build system: r
Synopsis: Transcription factor Inference through Gaussian process Reconstruction of Expression
Description:

The tigre package implements our methodology of Gaussian process differential equation models for analysis of gene expression time series from single input motif networks. The package can be used for inferring unobserved transcription factor (TF) protein concentrations from expression measurements of known target genes, or for ranking candidate targets of a TF.

r-tcc 1.50.0
Propagated dependencies: r-roc@1.86.0 r-edger@4.8.0 r-deseq2@1.50.2
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TCC
Licenses: GPL 2
Build system: r
Synopsis: TCC: Differential expression analysis for tag count data with robust normalization strategies
Description:

This package provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in depended packages.

r-txdb-celegans-ucsc-ce11-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.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-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-txdb-rnorvegicus-biomart-igis 2.3.2
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.BioMart.igis
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-tsar 1.8.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TSAR
Licenses: AGPL 3
Build system: r
Synopsis: Thermal Shift Analysis in R
Description:

This package automates analysis workflow for Thermal Shift Analysis (TSA) data. Processing, analyzing, and visualizing data through both shiny applications and command lines. Package aims to simplify data analysis and offer front to end workflow, from raw data to multiple trial analysis.

r-tabulamurissenisdata 1.16.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-hdf5array@1.38.0 r-gdata@3.0.1 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://github.com/fmicompbio/TabulaMurisSenisData
Licenses: Expat
Build system: r
Synopsis: Bulk and single-cell RNA-seq data from the Tabula Muris Senis project
Description:

This package provides access to RNA-seq data generated by the Tabula Muris Senis project via the Bioconductor project. The data is made available without restrictions by the Chan Zuckerberg Biohub. It is provided here without further processing, collected in the form of SingleCellExperiment objects.

r-txdb-athaliana-biomart-plantsmart51 0.99.0
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.Athaliana.BioMart.plantsmart51
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. This package is for Arabidopsis thaliana (taxID: 3702). The BioMart plantsmart release number is 51.

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-trajectorygeometry 1.18.0
Propagated dependencies: r-rgl@1.3.31 r-pracma@2.4.6 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TrajectoryGeometry
Licenses: Expat
Build system: r
Synopsis: This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns
Description:

Given a time series or pseudo-times series of gene expression data, we might wish to know: Do the changes in gene expression in these data exhibit directionality? Are there turning points in this directionality. Do different subsets of the data move in different directions? This package uses spherical geometry to probe these sorts of questions. In particular, if we are looking at (say) the first n dimensions of the PCA of gene expression, directionality can be detected as the clustering of points on the (n-1)-dimensional sphere.

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-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-tissuetreg 1.30.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/cimbusch/tissueTreg
Licenses: GPL 2+
Build system: r
Synopsis: TWGBS and RNA-seq data from tissue T regulatory cells from mice
Description:

The package provides ready to use epigenomes (obtained from TWGBS) and transcriptomes (RNA-seq) from various tissues as obtained in the study (Delacher and Imbusch 2017, PMID: 28783152). Regulatory T cells (Treg cells) perform two distinct functions: they maintain self-tolerance, and they support organ homeostasis by differentiating into specialized tissue Treg cells. The underlying dataset characterises the epigenetic and transcriptomic modifications for specialized tissue Treg cells.

r-tenet 1.2.0
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-tenxpbmcdata 1.28.0
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/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.

r-txdb-mmulatta-ucsc-rhemac8-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.Mmulatta.UCSC.rheMac8.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 1.30.0
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-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.

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Total results: 69112