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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-txdb-rnorvegicus-ucsc-rn6-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.Rnorvegicus.UCSC.rn6.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-ttmap 1.32.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-rgl@1.3.31 r-colorramps@2.3.4 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TTMap
Licenses: GPL 2
Build system: r
Synopsis: Two-Tier Mapper: a clustering tool based on topological data analysis
Description:

TTMap is a clustering method that groups together samples with the same deviation in comparison to a control group. It is specially useful when the data is small. It is parameter free.

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-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-txcutr 1.16.0
Propagated dependencies: r-txdbmaker@1.6.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-iranges@2.44.0 r-genomicranges@1.62.0 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-tidybulk 2.0.1
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-txdb-rnorvegicus-ucsc-rn5-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.Rnorvegicus.UCSC.rn5.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-twoddpcr 1.34.0
Propagated dependencies: r-shiny@1.11.1 r-scales@1.4.0 r-s4vectors@0.48.0 r-rcolorbrewer@1.1-3 r-hexbin@1.28.5 r-ggplot2@4.0.1 r-class@7.3-23
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: http://github.com/CRUKMI-ComputationalBiology/twoddpcr/
Licenses: GPL 3
Build system: r
Synopsis: Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules
Description:

The twoddpcr package takes Droplet Digital PCR (ddPCR) droplet amplitude data from Bio-Rad's QuantaSoft and can classify the droplets. A summary of the positive/negative droplet counts can be generated, which can then be used to estimate the number of molecules using the Poisson distribution. This is the first open source package that facilitates the automatic classification of general two channel ddPCR data. Previous work includes definetherain (Jones et al., 2014) and ddpcRquant (Trypsteen et al., 2015) which both handle one channel ddPCR experiments only. The ddpcr package available on CRAN (Attali et al., 2016) supports automatic gating of a specific class of two channel ddPCR experiments only.

r-tfutils 1.30.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-shiny@1.11.1 r-rsamtools@2.26.0 r-rjson@0.2.23 r-readxl@1.4.5 r-org-hs-eg-db@3.22.0 r-miniui@0.1.2 r-magrittr@2.0.4 r-httr@1.4.7 r-gseabase@1.72.0 r-genomicfiles@1.46.0 r-dt@0.34.0 r-dplyr@1.1.4 r-biocfilecache@3.0.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/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-treekor 1.18.0
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.

r-top 1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/Harry25R/TOP
Licenses: GPL 3
Build system: r
Synopsis: TOP Constructs Transferable Model Across Gene Expression Platforms
Description:

TOP constructs a transferable model across gene expression platforms for prospective experiments. Such a transferable model can be trained to make predictions on independent validation data with an accuracy that is similar to a re-substituted model. The TOP procedure also has the flexibility to be adapted to suit the most common clinical response variables, including linear response, binomial and Cox PH models.

r-tdbasedufe 1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/tagtag/TDbasedUFE
Licenses: GPL 3
Build system: r
Synopsis: Tensor Decomposition Based Unsupervised Feature Extraction
Description:

This is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. It can perform unsupervised feature extraction. It uses tensor decomposition. It is applicable to gene expression, DNA methylation, and histone modification etc. It can perform multiomics analysis. It is also potentially applicable to single cell omics data sets.

r-txdb-cfamiliaris-ucsc-canfam5-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.canFam5.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-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-teqc 4.32.0
Propagated dependencies: r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-iranges@2.44.0 r-hwriter@1.3.2.1 r-genomicranges@1.62.0 r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/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-terapadog 1.2.0
Propagated dependencies: r-plotly@4.11.0 r-keggrest@1.50.0 r-htmlwidgets@1.6.4 r-dplyr@1.1.4 r-deseq2@1.50.2 r-biomart@2.66.0
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-tinesath1cdf 1.48.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/tinesath1cdf
Licenses: Artistic License 2.0
Build system: r
Synopsis: tinesath1cdf
Description:

This package provides a package containing an environment represeting the newcdf/tinesATH1.cdf.cdf file.

r-txdb-ggallus-ucsc-galgal4-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.Ggallus.UCSC.galGal4.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-tomatoprobe 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/tomatoprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type tomato
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 Tomato\_probe\_tab.

r-txdb-rnorvegicus-ucsc-rn7-refgene 3.15.0
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.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-txdb-athaliana-biomart-plantsmart22 3.0.1
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.plantsmart22
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-transmogr 1.6.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-variantannotation@1.56.0 r-summarizedexperiment@1.40.0 r-seqinfo@1.0.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-patchwork@1.3.2 r-matrixstats@1.5.0 r-jsonlite@2.0.0 r-iranges@2.44.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-data-table@1.17.8 r-bsgenome@1.78.0 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/smped/transmogR
Licenses: GPL 3
Build system: r
Synopsis: Modify a set of reference sequences using a set of variants
Description:

transmogR provides the tools needed to crate a new reference genome or reference transcriptome, using a set of variants. Variants can be any combination of SNPs, Insertions and Deletions. The intended use-case is to enable creation of variant-modified reference transcriptomes for incorporation into transcriptomic pseudo-alignment workflows, such as salmon.

r-tcseq 1.34.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-rsamtools@2.26.0 r-reshape2@1.4.5 r-locfit@1.5-9.12 r-iranges@2.44.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicalignments@1.46.0 r-edger@4.8.0 r-e1071@1.7-16 r-cluster@2.1.8.1 r-biocgenerics@0.56.0
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-tinesath1probe 1.48.0
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/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.

Total results: 2911