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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.

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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-tenxbusdata 1.26.0
Propagated dependencies: r-experimenthub@3.2.0 r-biocgenerics@0.58.1 r-annotationhub@4.2.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/BUStools/TENxBUSData
Licenses: FreeBSD
Build system: r
Synopsis: Single cell dataset from 10x in BUS format
Description:

Download Barcode, UMI, and Set (BUS) format of 10x datasets from within R. This package accompanies the package BUSpaRse, which can load BUS format into R as a sparse matrix, and which has utility functions related to using the C++ command line package bustools.

r-txdb-rnorvegicus-ucsc-rn7-refgene 3.15.0
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.Rnorvegicus.UCSC.rn7.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-tscan 1.50.0
Propagated dependencies: r-trajectoryutils@1.20.0 r-summarizedexperiment@1.42.0 r-sparsearray@1.12.2 r-singlecellexperiment@1.34.0 r-shiny@1.13.0 r-s4vectors@0.50.1 r-plyr@1.8.9 r-mgcv@1.9-4 r-mclust@6.1.2 r-matrix@1.7-5 r-igraph@2.3.1 r-gplots@3.3.0 r-ggplot2@4.0.3 r-fastica@1.2-7 r-delayedarray@0.38.1 r-combinat@0.0-8
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TSCAN
Licenses: FSDG-compatible
Build system: r
Synopsis: Tools for Single-Cell Analysis
Description:

This package provides methods to perform trajectory analysis based on a minimum spanning tree constructed from cluster centroids. Computes pseudotemporal cell orderings by mapping cells in each cluster (or new cells) to the closest edge in the tree. Uses linear modelling to identify differentially expressed genes along each path through the tree. Several plotting and interactive visualization functions are also implemented.

r-tidybulk 2.2.0
Propagated dependencies: r-ttservice@0.5.3 r-tidyselect@1.2.1 r-tidyr@1.3.2 r-tibble@3.3.1 r-summarizedexperiment@1.42.0 r-stringr@1.6.0 r-scales@1.4.0 r-s4vectors@0.50.1 r-rlang@1.2.0 r-purrr@1.2.2 r-matrix@1.7-5 r-magrittr@2.0.5 r-lifecycle@1.0.5 r-ggplot2@4.0.3 r-genomicranges@1.64.0 r-dplyr@1.2.1 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-twilight 1.88.0
Propagated dependencies: r-biobase@2.72.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: http://compdiag.molgen.mpg.de/software/twilight.shtml
Licenses: GPL 2+
Build system: r
Synopsis: Estimation of local false discovery rate
Description:

In a typical microarray setting with gene expression data observed under two conditions, the local false discovery rate describes the probability that a gene is not differentially expressed between the two conditions given its corrresponding observed score or p-value level. The resulting curve of p-values versus local false discovery rate offers an insight into the twilight zone between clear differential and clear non-differential gene expression. Package twilight contains two main functions: Function twilight.pval performs a two-condition test on differences in means for a given input matrix or expression set and computes permutation based p-values. Function twilight performs a stochastic downhill search to estimate local false discovery rates and effect size distributions. The package further provides means to filter for permutations that describe the null distribution correctly. Using filtered permutations, the influence of hidden confounders could be diminished.

r-tofsimsdata 1.40.0
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-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-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-tripr 1.18.0
Propagated dependencies: r-vegan@2.7-3 r-stringr@1.6.0 r-stringdist@0.9.17 r-shinyjs@2.1.1 r-shinyfiles@0.9.3 r-shinybs@0.65.0 r-shiny@1.13.0 r-rcolorbrewer@1.1-3 r-plyr@1.8.9 r-plotly@4.12.0 r-plot3d@1.4.2 r-gridextra@2.3 r-golem@0.5.1 r-dt@0.34.0 r-dplyr@1.2.1 r-data-table@1.18.4 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-tidysinglecellexperiment 1.22.0
Propagated dependencies: r-vctrs@0.7.3 r-ttservice@0.5.3 r-tidyselect@1.2.1 r-tidyr@1.3.2 r-tibble@3.3.1 r-summarizedexperiment@1.42.0 r-stringr@1.6.0 r-singlecellexperiment@1.34.0 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-matrix@1.7-5 r-magrittr@2.0.5 r-lifecycle@1.0.5 r-ggplot2@4.0.3 r-fansi@1.0.7 r-ellipsis@0.3.3 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/stemangiola/tidySingleCellExperiment
Licenses: GPL 3
Build system: r
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-ternarynet 1.56.0
Propagated dependencies: r-igraph@2.3.1 r-biocparallel@1.46.0
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-txdb-rnorvegicus-ucsc-rn4-ensgene 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.Rnorvegicus.UCSC.rn4.ensGene
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-tiledbarray 1.22.0
Propagated dependencies: r-tiledb@0.33.0 r-sparsearray@1.12.2 r-s4vectors@0.50.1 r-delayedarray@0.38.1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/LTLA/TileDBArray
Licenses: Expat
Build system: r
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-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-txdb-rnorvegicus-biomart-igis 2.3.2
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.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-athaliana-biomart-plantsmart25 3.1.3
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.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-tumourmethdata 1.9.0
Propagated dependencies: r-summarizedexperiment@1.42.0 r-rhdf5@2.56.0 r-r-utils@2.13.0 r-hdf5array@1.40.0 r-genomicranges@1.64.0 r-experimenthub@3.2.0
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-tinesath1probe 1.50.0
Propagated dependencies: r-annotationdbi@1.74.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/tinesath1probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type tinesath1
Description:

This package was automatically created by package matchprobes version 1.4.0. The probe sequence data was obtained from http://www.affymetrix.com.

r-transomics2cytoscape 1.22.0
Propagated dependencies: r-tibble@3.3.1 r-rcy3@2.32.0 r-purrr@1.2.2 r-pbapply@1.7-4 r-keggrest@1.52.0 r-dplyr@1.2.1
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-txdb-sscrofa-ucsc-susscr3-refgene 3.12.0
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.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-tomoda 1.22.0
Propagated dependencies: r-umap@0.2.10.0 r-summarizedexperiment@1.42.0 r-rtsne@0.17 r-reshape2@1.4.5 r-rcolorbrewer@1.1-3 r-ggrepel@0.9.8 r-ggplot2@4.0.3
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/liuwd15/tomoda
Licenses: Expat
Build system: r
Synopsis: Tomo-seq data analysis
Description:

This package provides many easy-to-use methods to analyze and visualize tomo-seq data. The tomo-seq technique is based on cryosectioning of tissue and performing RNA-seq on consecutive sections. (Reference: Kruse F, Junker JP, van Oudenaarden A, Bakkers J. Tomo-seq: A method to obtain genome-wide expression data with spatial resolution. Methods Cell Biol. 2016;135:299-307. doi:10.1016/bs.mcb.2016.01.006) The main purpose of the package is to find zones with similar transcriptional profiles and spatially expressed genes in a tomo-seq sample. Several visulization functions are available to create easy-to-modify plots.

r-txdb-sscrofa-ucsc-susscr11-refgene 3.12.0
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.Sscrofa.UCSC.susScr11.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-treekor 1.20.0
Propagated dependencies: r-tidyr@1.3.2 r-singlecellexperiment@1.34.0 r-patchwork@1.3.2 r-multcomp@1.4-30 r-lme4@2.0-1 r-hopach@2.72.0 r-ggtree@4.2.0 r-ggplot2@4.0.3 r-ggiraph@0.9.6 r-edger@4.10.0 r-dplyr@1.2.1 r-diffcyt@1.32.0 r-data-table@1.18.4 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/treekoR
Licenses: GPL 3
Build system: r
Synopsis: Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations
Description:

treekoR is a novel framework that aims to utilise the hierarchical nature of single cell cytometry data to find robust and interpretable associations between cell subsets and patient clinical end points. These associations are aimed to recapitulate the nested proportions prevalent in workflows inovlving manual gating, which are often overlooked in workflows using automatic clustering to identify cell populations. We developed treekoR to: Derive a hierarchical tree structure of cell clusters; quantify a cell types as a proportion relative to all cells in a sample (%total), and, as the proportion relative to a parent population (%parent); perform significance testing using the calculated proportions; and provide an interactive html visualisation to help highlight key results.

Total packages: 3017