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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-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-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-ptroglodytes-ucsc-pantro4-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.panTro4.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-tidysbml 1.4.0
Propagated dependencies: r-xml2@1.5.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/veronicapaparozzi/tidysbml
Licenses: FSDG-compatible
Build system: r
Synopsis: Extract SBML's data into dataframes
Description:

Starting from one SBML file, it extracts information from each listOfCompartments, listOfSpecies and listOfReactions element by saving them into data frames. Each table provides one row for each entity (i.e. either compartment, species, reaction or speciesReference) and one set of columns for the attributes, one column for the content of the notes subelement and one set of columns for the content of the annotation subelement.

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-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).

r-txdb-mmulatta-ucsc-rhemac3-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.rheMac3.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-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-txdb-btaurus-ucsc-bostau8-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.Btaurus.UCSC.bosTau8.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-tenxbraindata 1.30.0
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-tadar 1.8.0
Propagated dependencies: r-variantannotation@1.56.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-rlang@1.1.6 r-matrixgenerics@1.22.0 r-lifecycle@1.0.4 r-iranges@2.44.0 r-gviz@1.54.0 r-ggplot2@4.0.1 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/baerlachlan/tadar
Licenses: GPL 3
Build system: r
Synopsis: Transcriptome Analysis of Differential Allelic Representation
Description:

This package provides functions to standardise the analysis of Differential Allelic Representation (DAR). DAR compromises the integrity of Differential Expression analysis results as it can bias expression, influencing the classification of genes (or transcripts) as being differentially expressed. DAR analysis results in an easy-to-interpret value between 0 and 1 for each genetic feature of interest, where 0 represents identical allelic representation and 1 represents complete diversity. This metric can be used to identify features prone to false-positive calls in Differential Expression analysis, and can be leveraged with statistical methods to alleviate the impact of such artefacts on RNA-seq data.

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-txdb-hsapiens-ucsc-hg18-knowngene 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.Hsapiens.UCSC.hg18.knownGene
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-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-tscan 1.48.0
Propagated dependencies: r-trajectoryutils@1.18.0 r-summarizedexperiment@1.40.0 r-sparsearray@1.10.2 r-singlecellexperiment@1.32.0 r-shiny@1.11.1 r-s4vectors@0.48.0 r-plyr@1.8.9 r-mgcv@1.9-4 r-mclust@6.1.2 r-matrix@1.7-4 r-igraph@2.2.1 r-gplots@3.2.0 r-ggplot2@4.0.1 r-fastica@1.2-7 r-delayedarray@0.36.0 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-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-topdownrdata 1.32.0
Propagated dependencies: r-topdownr@1.32.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://codeberg.org/sgibb/topdownrdata/
Licenses: GPL 3+
Build system: r
Synopsis: Example Files for the topdownr R Package
Description:

Example data for the topdownr package generated on a Thermo Orbitrap Fusion Lumos MS device.

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-tenet 1.2.0
Propagated dependencies: r-tenet-experimenthub@1.2.0 r-tcgabiolinks@2.38.0 r-survminer@0.5.1 r-survival@3.8-3 r-summarizedexperiment@1.40.0 r-sesamedata@1.28.0 r-sesame@1.28.0 r-seqlogo@1.76.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rcircos@1.2.2 r-r-utils@2.13.0 r-pastecs@1.4.2 r-multiassayexperiment@1.36.1 r-motifdb@1.52.0 r-matlab@1.0.4.1 r-iranges@2.44.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-experimenthub@3.0.0 r-bsgenome-hsapiens-ucsc-hg38@1.4.5 r-biostrings@2.78.0 r-bammtools@2.1.12 r-annotationhub@4.0.0
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-transcriptogramer 1.32.0
Propagated dependencies: r-topgo@2.62.0 r-tidyr@1.3.1 r-snow@0.4-4 r-reder@3.6.0 r-progress@1.2.3 r-limma@3.66.0 r-igraph@2.2.1 r-ggplot2@4.0.1 r-foreach@1.5.2 r-dosnow@1.0.20 r-data-table@1.17.8 r-biomart@2.66.0
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-tidybulk 2.0.1
Propagated dependencies: r-ttservice@0.5.3 r-tidyselect@1.2.1 r-tidyr@1.3.1 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-rlang@1.1.6 r-purrr@1.2.0 r-matrix@1.7-4 r-magrittr@2.0.4 r-lifecycle@1.0.4 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-dplyr@1.1.4 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-tenxvisiumdata 1.18.0
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-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.

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Total results: 68655