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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-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-targetscore 1.50.0
Propagated dependencies: r-pracma@2.4.6 r-matrix@1.7-4
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: http://www.cs.utoronto.ca/~yueli/software.html
Licenses: GPL 2
Build system: r
Synopsis: TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information
Description:

Infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. Variaitonal Bayesian Gaussian mixture model (VB-GMM) is applied to log fold-changes and sequence scores to obtain the posteriors of latent variable being the miRNA targets. The final targetScore is computed as the sigmoid-transformed fold-change weighted by the averaged posteriors of target components over all of the features.

r-txdb-athaliana-biomart-plantsmart28 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.Athaliana.BioMart.plantsmart28
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-terapadog 1.4.0
Propagated dependencies: r-plotly@4.12.0 r-keggrest@1.50.0 r-htmlwidgets@1.6.4 r-dplyr@1.2.0 r-deseq2@1.50.2 r-biomart@2.66.1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/Gionmattia/terapadog
Licenses: GPL 2
Build system: r
Synopsis: Translational Efficiency Regulation Analysis using the PADOG Method
Description:

This package performs a Gene Set Analysis with the approach adopted by PADOG on the genes that are reported as translationally regulated (ie. exhibit a significant change in TE) by the DeltaTE package. It can be used on its own to see the impact of translation regulation on gene sets, but it is also integrated as an additional analysis method within ReactomeGSA, where results are further contextualised in terms of pathways and directionality of the change.

r-tmixclust 1.34.0
Propagated dependencies: r-zoo@1.8-15 r-spem@1.52.0 r-mvtnorm@1.3-3 r-gss@2.2-10 r-flexclust@1.5.0 r-cluster@2.1.8.2 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-transcriptogramer 1.34.0
Propagated dependencies: r-topgo@2.62.0 r-tidyr@1.3.2 r-snow@0.4-4 r-reder@3.8.0 r-progress@1.2.3 r-limma@3.66.0 r-igraph@2.2.2 r-ggplot2@4.0.2 r-foreach@1.5.2 r-dosnow@1.0.20 r-data-table@1.18.2.1 r-biomart@2.66.1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/arthurvinx/transcriptogramer
Licenses: GPL 2+
Build system: r
Synopsis: Transcriptional analysis based on transcriptograms
Description:

R package for transcriptional analysis based on transcriptograms, a method to analyze transcriptomes that projects expression values on a set of ordered proteins, arranged such that the probability that gene products participate in the same metabolic pathway exponentially decreases with the increase of the distance between two proteins of the ordering. Transcriptograms are, hence, genome wide gene expression profiles that provide a global view for the cellular metabolism, while indicating gene sets whose expressions are altered.

r-taxsea 1.4.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/feargalr/taxsea
Licenses: GPL 3
Build system: r
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-transformgampoi 1.18.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-rcpp@1.1.1 r-matrixgenerics@1.22.0 r-matrix@1.7-4 r-hdf5array@1.38.0 r-glmgampoi@1.22.0 r-delayedarray@0.36.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/const-ae/transformGamPoi
Licenses: GPL 3
Build system: r
Synopsis: Variance Stabilizing Transformation for Gamma-Poisson Models
Description:

Variance-stabilizing transformations help with the analysis of heteroskedastic data (i.e., data where the variance is not constant, like count data). This package provide two types of variance stabilizing transformations: (1) methods based on the delta method (e.g., acosh', log(x+1)'), (2) model residual based (Pearson and randomized quantile residuals).

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-txdb-btaurus-ucsc-bostau9-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.Btaurus.UCSC.bosTau9.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-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-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-txcutr 1.18.0
Propagated dependencies: r-txdbmaker@1.6.2 r-s4vectors@0.48.0 r-rtracklayer@1.70.1 r-iranges@2.44.0 r-genomicranges@1.62.1 r-genomicfeatures@1.62.0 r-biostrings@2.78.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/mfansler/txcutr
Licenses: GPL 3
Build system: r
Synopsis: Transcriptome CUTteR
Description:

Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can be aided by using truncated versions of transcriptome annotations, both at the alignment or pseudo-alignment stage, as well as in downstream analysis. This package implements some convenience methods for readily generating such truncated annotations and their corresponding sequences.

r-tidysummarizedexperiment 1.22.0
Propagated dependencies: r-vctrs@0.7.1 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-s4vectors@0.48.0 r-rlang@1.1.7 r-purrr@1.2.1 r-plyxp@1.6.1 r-pkgconfig@2.0.3 r-pillar@1.11.1 r-magrittr@2.0.4 r-lifecycle@1.0.5 r-ggplot2@4.0.2 r-fansi@1.0.7 r-ellipsis@0.3.2 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/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-trnascanimport 1.32.0
Propagated dependencies: r-xvector@0.50.0 r-trna@1.28.0 r-structstrings@1.26.0 r-stringr@1.6.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.1 r-rsamtools@2.26.0 r-iranges@2.44.0 r-genomicranges@1.62.1 r-bsgenome@1.78.0 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://github.com/FelixErnst/tRNAscanImport
Licenses: FSDG-compatible
Build system: r
Synopsis: Importing a tRNAscan-SE result file as GRanges object
Description:

The package imports the result of tRNAscan-SE as a GRanges object.

r-turbonorm 1.60.0
Propagated dependencies: r-marray@1.88.0 r-limma@3.66.0 r-lattice@0.22-9 r-convert@1.86.0 r-affy@1.88.0
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+
Build system: r
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-txdb-ptroglodytes-ucsc-pantro5-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.Ptroglodytes.UCSC.panTro5.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-hsapiens-ucsc-hg38-refgene 3.19.0
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.Hsapiens.UCSC.hg38.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-ternarynet 1.56.0
Propagated dependencies: r-igraph@2.2.2 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/ternarynet
Licenses: GPL 2+
Build system: r
Synopsis: Ternary Network Estimation
Description:

Gene-regulatory network (GRN) modeling seeks to infer dependencies between genes and thereby provide insight into the regulatory relationships that exist within a cell. This package provides a computational Bayesian approach to GRN estimation from perturbation experiments using a ternary network model, in which gene expression is discretized into one of 3 states: up, unchanged, or down). The ternarynet package includes a parallel implementation of the replica exchange Monte Carlo algorithm for fitting network models, using MPI.

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-tidyflowcore 1.6.0
Propagated dependencies: r-tidyr@1.3.2 r-tibble@3.3.1 r-stringr@1.6.0 r-rlang@1.1.7 r-purrr@1.2.1 r-ggplot2@4.0.2 r-flowcore@2.22.1 r-dplyr@1.2.0 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-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-test3probe 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/test3probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type test3
Description:

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Test3\_probe\_tab.

r-tpp2d 1.28.0
Propagated dependencies: r-tidyr@1.3.2 r-stringr@1.6.0 r-rcurl@1.98-1.17 r-openxlsx@4.2.8.1 r-mass@7.3-65 r-limma@3.66.0 r-ggplot2@4.0.2 r-foreach@1.5.2 r-dplyr@1.2.0 r-doparallel@1.0.17 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: http://bioconductor.org/packages/TPP2D
Licenses: GPL 3
Build system: r
Synopsis: Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)
Description:

Detection of ligand-protein interactions from 2D thermal profiles (DLPTP), Performs an FDR-controlled analysis of 2D-TPP experiments by functional analysis of dose-response curves across temperatures.

Total packages: 3017