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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-tapseq 1.22.1
Dependencies: blast+@2.17.0
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-treg 1.14.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-rafalib@1.0.4 r-purrr@1.2.0 r-matrix@1.7-4
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/LieberInstitute/TREG
Licenses: Artistic License 2.0
Build system: r
Synopsis: Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
Description:

RNA abundance and cell size parameters could improve RNA-seq deconvolution algorithms to more accurately estimate cell type proportions given the different cell type transcription activity levels. A Total RNA Expression Gene (TREG) can facilitate estimating total RNA content using single molecule fluorescent in situ hybridization (smFISH). We developed a data-driven approach using a measure of expression invariance to find candidate TREGs in postmortem human brain single nucleus RNA-seq. This R package implements the method for identifying candidate TREGs from snRNA-seq data.

r-tweedeseq 1.56.0
Propagated dependencies: r-rcpp@1.1.0 r-mass@7.3-65 r-limma@3.66.0 r-edger@4.8.0 r-cqn@1.56.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/isglobal-brge/tweeDEseq/
Licenses: GPL 2+
Build system: r
Synopsis: RNA-seq data analysis using the Poisson-Tweedie family of distributions
Description:

Differential expression analysis of RNA-seq using the Poisson-Tweedie (PT) family of distributions. PT distributions are described by a mean, a dispersion and a shape parameter and include Poisson and NB distributions, among others, as particular cases. An important feature of this family is that, while the Negative Binomial (NB) distribution only allows a quadratic mean-variance relationship, the PT distributions generalizes this relationship to any orde.

r-transite 1.28.0
Propagated dependencies: r-tfmpvalue@0.0.9 r-stringr@1.6.0 r-scales@1.4.0 r-rcpp@1.1.0 r-gridextra@2.3 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-dplyr@1.1.4 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://transite.mit.edu
Licenses: Expat
Build system: r
Synopsis: RNA-binding protein motif analysis
Description:

transite is a computational method that allows comprehensive analysis of the regulatory role of RNA-binding proteins in various cellular processes by leveraging preexisting gene expression data and current knowledge of binding preferences of RNA-binding proteins.

r-tpp 3.38.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TPP
Licenses: Artistic License 2.0
Build system: r
Synopsis: Analyze thermal proteome profiling (TPP) experiments
Description:

Analyze thermal proteome profiling (TPP) experiments with varying temperatures (TR) or compound concentrations (CCR).

r-tbx20bamsubset 1.46.0
Propagated dependencies: r-xtable@1.8-4 r-rsamtools@2.26.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TBX20BamSubset
Licenses: LGPL 2.0+
Build system: r
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-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-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-txdb-drerio-ucsc-danrer11-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.danRer11.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-toxicogx 2.14.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/ToxicoGx
Licenses: Expat
Build system: r
Synopsis: Analysis of Large-Scale Toxico-Genomic Data
Description:

This package contains a set of functions to perform large-scale analysis of toxicogenomic data, providing a standardized data structure to hold information relevant to annotation, visualization and statistical analysis of toxicogenomic data.

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-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-test1cdf 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/test1cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: test1cdf
Description:

This package provides a package containing an environment representing the Test1.CDF file.

r-trnascanimport 1.30.0
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@1.70.0 r-rsamtools@2.26.0 r-iranges@2.44.0 r-genomicranges@1.62.0 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-tidyomics 1.6.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/tidyomics/tidyomics
Licenses: Expat
Build system: r
Synopsis: Easily install and load the tidyomics ecosystem
Description:

The tidyomics ecosystem is a set of packages for ’omic data analysis that work together in harmony; they share common data representations and API design, consistent with the tidyverse ecosystem. The tidyomics package is designed to make it easy to install and load core packages from the tidyomics ecosystem with a single command.

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-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-tuberculosis 1.16.0
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
Build system: r
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-topconfects 1.26.0
Propagated dependencies: r-scales@1.4.0 r-ggplot2@4.0.1 r-assertthat@0.2.1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/pfh/topconfects
Licenses: LGPL 2.1 FSDG-compatible
Build system: r
Synopsis: Top Confident Effect Sizes
Description:

Rank results by confident effect sizes, while maintaining False Discovery Rate and False Coverage-statement Rate control. Topconfects is an alternative presentation of TREAT results with improved usability, eliminating p-values and instead providing confidence bounds. The main application is differential gene expression analysis, providing genes ranked in order of confident log2 fold change, but it can be applied to any collection of effect sizes with associated standard errors.

r-translatome 1.48.0
Propagated dependencies: r-topgo@2.62.0 r-rankprod@3.36.0 r-plotrix@3.8-13 r-org-hs-eg-db@3.22.0 r-limma@3.66.0 r-heatplus@3.18.0 r-gplots@3.2.0 r-gosemsim@2.36.0 r-edger@4.8.0 r-deseq2@1.50.2 r-biobase@2.70.0 r-anota@1.58.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/tRanslatome
Licenses: GPL 3
Build system: r
Synopsis: Comparison between multiple levels of gene expression
Description:

Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions (treated vs. untreated, diseased vs. normal, mutant vs. wild-type) among different levels of gene expression (transcriptome ,translatome, proteome), using several statistical methods: Rank Product, Translational Efficiency, t-test, Limma, ANOTA, DESeq, edgeR. Possibility to plot the results with scatterplots, histograms, MA plots, standard deviation (SD) plots, coefficient of variation (CV) plots. Detection of significantly enriched post-transcriptional regulatory factors (RBPs, miRNAs, etc) and Gene Ontology terms in the lists of DEGs previously identified for the two expression levels. Comparison of GO terms enriched only in one of the levels or in both. Calculation of the semantic similarity score between the lists of enriched GO terms coming from the two expression levels. Visual examination and comparison of the enriched terms with heatmaps, radar plots and barplots.

r-tfarm 1.32.0
Propagated dependencies: r-stringr@1.6.0 r-gplots@3.2.0 r-genomicranges@1.62.0 r-fields@17.1 r-arules@1.7-11
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TFARM
Licenses: Artistic License 2.0
Build system: r
Synopsis: Transcription Factors Association Rules Miner
Description:

It searches for relevant associations of transcription factors with a transcription factor target, in specific genomic regions. It also allows to evaluate the Importance Index distribution of transcription factors (and combinations of transcription factors) in association rules.

r-txdb-rnorvegicus-ucsc-rn6-ncbirefseq 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.Rnorvegicus.UCSC.rn6.ncbiRefSeq
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-cfamiliaris-ucsc-canfam4-refgene 3.14.0
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.Cfamiliaris.UCSC.canFam4.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-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
Build system: r
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).

Total results: 2911