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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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r-tissueenrich 1.32.0
Propagated dependencies: r-tidyr@1.3.2 r-summarizedexperiment@1.40.0 r-gseabase@1.72.0 r-ggplot2@4.0.2 r-dplyr@1.2.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TissueEnrich
Licenses: Expat
Build system: r
Synopsis: Tissue-specific gene enrichment analysis
Description:

The TissueEnrich package is used to calculate enrichment of tissue-specific genes in a set of input genes. For example, the user can input the most highly expressed genes from RNA-Seq data, or gene co-expression modules to determine which tissue-specific genes are enriched in those datasets. Tissue-specific genes were defined by processing RNA-Seq data from the Human Protein Atlas (HPA) (Uhlén et al. 2015), GTEx (Ardlie et al. 2015), and mouse ENCODE (Shen et al. 2012) using the algorithm from the HPA (Uhlén et al. 2015).The hypergeometric test is being used to determine if the tissue-specific genes are enriched among the input genes. Along with tissue-specific gene enrichment, the TissueEnrich package can also be used to define tissue-specific genes from expression datasets provided by the user, which can then be used to calculate tissue-specific gene enrichments.

r-tadar 1.10.0
Propagated dependencies: r-variantannotation@1.56.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-rlang@1.1.7 r-matrixgenerics@1.22.0 r-lifecycle@1.0.5 r-iranges@2.44.0 r-gviz@1.54.0 r-ggplot2@4.0.2 r-genomicranges@1.62.1 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-tinesath1probe 1.50.0
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.

r-toxicogx 2.16.0
Propagated dependencies: r-tidyr@1.3.2 r-tibble@3.3.1 r-summarizedexperiment@1.40.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-reshape2@1.4.5 r-magrittr@2.0.4 r-limma@3.66.0 r-jsonlite@2.0.0 r-ggplot2@4.0.2 r-dplyr@1.2.0 r-downloader@0.4.1 r-data-table@1.18.2.1 r-coregx@2.14.0 r-catools@1.18.3 r-biocparallel@1.44.0 r-biocgenerics@0.56.0 r-biobase@2.70.0 r-assertthat@0.2.1
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-treeandleaf 1.24.0
Propagated dependencies: r-reder@3.8.0 r-igraph@2.2.2 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://doi.org/10.1093/bioinformatics/btab819
Licenses: Artistic License 2.0
Build system: r
Synopsis: Displaying binary trees with focus on dendrogram leaves
Description:

TreeAndLeaf implements a hybrid layout strategy that enhances leaf-level visualization in dendrograms. By integrating force-directed graph and tree layout algorithms, it enables projection of multiple layers of information onto graph–tree diagrams.

r-txdb-cfamiliaris-ucsc-canfam6-refgene 3.17.0
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.canFam6.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-tcgamethylation450k 1.48.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TCGAMethylation450k
Licenses: GPL 2
Build system: r
Synopsis: The Cancer Genome Atlas Illumina 450k methylation example data
Description:

The Cancer Genome Atlas (TCGA) is applying genomics technologies to over 20 different types of cancer. This package contains a small set of 450k array data in idat format.

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-tomoseqr 1.16.0
Propagated dependencies: r-tibble@3.3.1 r-stringr@1.6.0 r-shiny@1.11.1 r-readr@2.2.0 r-purrr@1.2.1 r-plotly@4.12.0 r-ggplot2@4.0.2 r-dplyr@1.2.0 r-biocfilecache@3.0.0 r-animation@2.8
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-tloh 1.19.0
Propagated dependencies: r-variantannotation@1.56.0 r-stringr@1.6.0 r-scales@1.4.0 r-purrr@1.2.1 r-naniar@1.1.0 r-matrixgenerics@1.22.0 r-ggplot2@4.0.2 r-genomicranges@1.62.1 r-dplyr@1.2.0 r-depmixs4@1.5-1 r-data-table@1.18.2.1 r-bestnormalize@1.9.2
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/USCDTG/tLOH
Licenses: Expat
Build system: r
Synopsis: Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations
Description:

tLOH, or transcriptomicsLOH, assesses evidence for loss of heterozygosity (LOH) in pre-processed spatial transcriptomics data. This tool requires spatial transcriptomics cluster and allele count information at likely heterozygous single-nucleotide polymorphism (SNP) positions in VCF format. Bayes factors are calculated at each SNP to determine likelihood of potential loss of heterozygosity event. Two plotting functions are included to visualize allele fraction and aggregated Bayes factor per chromosome. Data generated with the 10X Genomics Visium Spatial Gene Expression platform must be pre-processed to obtain an individual sample VCF with columns for each cluster. Required fields are allele depth (AD) with counts for reference/alternative alleles and read depth (DP).

r-tapseq 1.24.0
Dependencies: blast+@2.17.0
Propagated dependencies: r-tidyr@1.3.2 r-s4vectors@0.48.0 r-iranges@2.44.0 r-genomicranges@1.62.1 r-genomicfeatures@1.62.0 r-genomicalignments@1.46.0 r-genomeinfodb@1.46.2 r-dplyr@1.2.0 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0
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-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-trio 3.50.0
Propagated dependencies: r-survival@3.8-6 r-siggenes@1.84.0 r-logicreg@1.6.6 r-data-table@1.18.2.1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/trio
Licenses: LGPL 2.0
Build system: r
Synopsis: Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
Description:

Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.

r-tcgacrcmirna 1.32.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TCGAcrcmiRNA
Licenses: GPL 2
Build system: r
Synopsis: TCGA CRC 450 miRNA dataset
Description:

colorectal cancer miRNA profile provided by TCGA.

r-txdb-mmulatta-ucsc-rhemac8-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.rheMac8.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-tbx20bamsubset 1.48.0
Propagated dependencies: r-xtable@1.8-8 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-sscrofa-ucsc-susscr11-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.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-teqc 4.34.0
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@1.62.1 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-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-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@4.0.2 r-dplyr@1.2.0
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-tadcompare 1.22.0
Propagated dependencies: r-tidyr@1.3.2 r-reshape2@1.4.5 r-rcolorbrewer@1.1-3 r-matrix@1.7-4 r-magrittr@2.0.4 r-hiccompare@1.34.0 r-ggpubr@0.6.3 r-ggplot2@4.0.2 r-dplyr@1.2.0 r-cowplot@1.2.0 r-cluster@2.1.8.2
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/dozmorovlab/TADCompare
Licenses: Expat
Build system: r
Synopsis: TADCompare: Identification and characterization of differential TADs
Description:

TADCompare is an R package designed to identify and characterize differential Topologically Associated Domains (TADs) between multiple Hi-C contact matrices. It contains functions for finding differential TADs between two datasets, finding differential TADs over time and identifying consensus TADs across multiple matrices. It takes all of the main types of HiC input and returns simple, comprehensive, easy to analyze results.

r-tripr 1.18.0
Propagated dependencies: r-vegan@2.7-2 r-stringr@1.6.0 r-stringdist@0.9.17 r-shinyjs@2.1.1 r-shinyfiles@0.9.3 r-shinybs@0.63.0 r-shiny@1.11.1 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@1.2.0 r-data-table@1.18.2.1 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-txdb-celegans-ucsc-ce11-ensgene 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.Celegans.UCSC.ce11.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-test2cdf 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/test2cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: test2cdf
Description:

This package provides a package containing an environment representing the Test2.CDF file.

Total packages: 3017