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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-sitepath 1.26.0
Propagated dependencies: r-tidytree@0.4.6 r-seqinr@4.2-36 r-rcpp@1.1.0 r-rcolorbrewer@1.1-3 r-gridextra@2.3 r-ggtree@4.0.1 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-aplot@0.2.9 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://wuaipinglab.github.io/sitePath/
Licenses: Expat
Build system: r
Synopsis: Phylogeny-based sequence clustering with site polymorphism
Description:

Using site polymorphism is one of the ways to cluster DNA/protein sequences but it is possible for the sequences with the same polymorphism on a single site to be genetically distant. This package is aimed at clustering sequences using site polymorphism and their corresponding phylogenetic trees. By considering their location on the tree, only the structurally adjacent sequences will be clustered. However, the adjacent sequences may not necessarily have the same polymorphism. So a branch-and-bound like algorithm is used to minimize the entropy representing the purity of site polymorphism of each cluster.

r-scdotplot 1.4.0
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.3.0 r-stringr@1.6.0 r-singlecellexperiment@1.32.0 r-seurat@5.3.1 r-scater@1.38.0 r-scales@1.4.0 r-rlang@1.1.6 r-purrr@1.2.0 r-magrittr@2.0.4 r-ggtree@4.0.1 r-ggsci@4.1.0 r-ggplot2@4.0.1 r-dplyr@1.1.4 r-cli@3.6.5 r-biocgenerics@0.56.0 r-aplot@0.2.9
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/ben-laufer/scDotPlot
Licenses: Artistic License 2.0
Build system: r
Synopsis: Cluster a Single-cell RNA-seq Dot Plot
Description:

Dot plots of single-cell RNA-seq data allow for an examination of the relationships between cell groupings (e.g. clusters) and marker gene expression. The scDotPlot package offers a unified approach to perform a hierarchical clustering analysis and add annotations to the columns and/or rows of a scRNA-seq dot plot. It works with SingleCellExperiment and Seurat objects as well as data frames.

r-screclassify 1.16.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-randomforest@4.7-1.2 r-e1071@1.7-16
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/SydneyBioX/scReClassify
Licenses: FSDG-compatible
Build system: r
Synopsis: scReClassify: post hoc cell type classification of single-cell RNA-seq data
Description:

This package provides a post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure with semi-supervised learning algorithm AdaSampling technique. The current version of scReClassify supports Support Vector Machine and Random Forest as a base classifier.

r-synlet 2.10.0
Propagated dependencies: r-rcolorbrewer@1.1-3 r-rankprod@3.36.0 r-patchwork@1.3.2 r-magrittr@2.0.4 r-ggplot2@4.0.1 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/synlet
Licenses: GPL 3
Build system: r
Synopsis: Hits Selection for Synthetic Lethal RNAi Screen Data
Description:

Select hits from synthetic lethal RNAi screen data. For example, there are two identical celllines except one gene is knocked-down in one cellline. The interest is to find genes that lead to stronger lethal effect when they are knocked-down further by siRNA. Quality control and various visualisation tools are implemented. Four different algorithms could be used to pick up the interesting hits. This package is designed based on 384 wells plates, but may apply to other platforms with proper configuration.

r-specond 1.64.0
Propagated dependencies: r-rcolorbrewer@1.1-3 r-mclust@6.1.2 r-hwriter@1.3.2.1 r-fields@17.1 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/SpeCond
Licenses: FSDG-compatible
Build system: r
Synopsis: Condition specific detection from expression data
Description:

This package performs a gene expression data analysis to detect condition-specific genes. Such genes are significantly up- or down-regulated in a small number of conditions. It does so by fitting a mixture of normal distributions to the expression values. Conditions can be environmental conditions, different tissues, organs or any other sources that you wish to compare in terms of gene expression.

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-test3probe 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/test3probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type test3
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 Test3\_probe\_tab.

r-tomoseqr 1.14.0
Propagated dependencies: r-tibble@3.3.0 r-stringr@1.6.0 r-shiny@1.11.1 r-readr@2.1.6 r-purrr@1.2.0 r-plotly@4.11.0 r-ggplot2@4.0.1 r-dplyr@1.1.4 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-tenxio 1.12.1
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rhdf5@2.54.0 r-readr@2.1.6 r-rcurl@1.98-1.17 r-r-utils@2.13.0 r-matrixgenerics@1.22.0 r-matrix@1.7-4 r-hdf5array@1.38.0 r-genomicranges@1.62.0 r-biocio@1.20.0 r-biocgenerics@0.56.0 r-biocbaseutils@1.12.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/waldronlab/TENxIO
Licenses: Artistic License 2.0
Build system: r
Synopsis: Import methods for 10X Genomics files
Description:

This package provides a structured S4 approach to importing data files from the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene Expression data among other data types. The main Bioconductor data representations used are SingleCellExperiment and RaggedExperiment.

r-timescape 1.34.0
Propagated dependencies: r-stringr@1.6.0 r-jsonlite@2.0.0 r-htmlwidgets@1.6.4 r-gtools@3.9.5 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/timescape
Licenses: GPL 3
Build system: r
Synopsis: Patient Clonal Timescapes
Description:

TimeScape is an automated tool for navigating temporal clonal evolution data. The key attributes of this implementation involve the enumeration of clones, their evolutionary relationships and their shifting dynamics over time. TimeScape requires two inputs: (i) the clonal phylogeny and (ii) the clonal prevalences. Optionally, TimeScape accepts a data table of targeted mutations observed in each clone and their allele prevalences over time. The output is the TimeScape plot showing clonal prevalence vertically, time horizontally, and the plot height optionally encoding tumour volume during tumour-shrinking events. At each sampling time point (denoted by a faint white line), the height of each clone accurately reflects its proportionate prevalence. These prevalences form the anchors for bezier curves that visually represent the dynamic transitions between time points.

r-ttgsea 1.18.0
Propagated dependencies: r-tokenizers@0.3.0 r-tm@0.7-16 r-textstem@0.1.4 r-text2vec@0.6.4 r-stopwords@2.3 r-purrr@1.2.0 r-keras@2.16.0 r-diagrammer@1.0.11 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/ttgsea
Licenses: Artistic License 2.0
Build system: r
Synopsis: Tokenizing Text of Gene Set Enrichment Analysis
Description:

Functional enrichment analysis methods such as gene set enrichment analysis (GSEA) have been widely used for analyzing gene expression data. GSEA is a powerful method to infer results of gene expression data at a level of gene sets by calculating enrichment scores for predefined sets of genes. GSEA depends on the availability and accuracy of gene sets. There are overlaps between terms of gene sets or categories because multiple terms may exist for a single biological process, and it can thus lead to redundancy within enriched terms. In other words, the sets of related terms are overlapping. Using deep learning, this pakage is aimed to predict enrichment scores for unique tokens or words from text in names of gene sets to resolve this overlapping set issue. Furthermore, we can coin a new term by combining tokens and find its enrichment score by predicting such a combined tokens.

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-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-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-tress 1.16.0
Propagated dependencies: r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rsamtools@2.26.0 r-matrixstats@1.5.0 r-matrix@1.7-4 r-iranges@2.44.0 r-genomicranges@1.62.0 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/TRESS
Licenses: FSDG-compatible
Build system: r
Synopsis: Toolbox for mRNA epigenetics sequencing analysis
Description:

This package is devoted to analyzing MeRIP-seq data. Current functionalities include 1. detect transcriptome wide m6A methylation regions 2. detect transcriptome wide differential m6A methylation regions.

r-tenet-annotationhub 1.1.0
Propagated dependencies: r-genomicranges@1.62.0 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.AnnotationHub
Licenses: GPL 2
Build system: r
Synopsis: Annotation data for the TENET package
Description:

AnnotationHub package containing datasets for use in the TENET package. Includes GenomicRanges objects representing putative enhancer, promoter, and open chromatin regions. All included datasets are aligned to the hg38 human genome.

r-targetsearch 2.12.0
Propagated dependencies: r-ncdf4@1.24 r-assertthat@0.2.1
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/acinostroza/TargetSearch
Licenses: GPL 2+
Build system: r
Synopsis: package for the analysis of GC-MS metabolite profiling data
Description:

This packages provides a flexible, fast and accurate method for targeted pre-processing of GC-MS data. The user provides a (often very large) set of GC chromatograms and a metabolite library of targets. The package will automatically search those targets in the chromatograms resulting in a data matrix that can be used for further data analysis.

r-tnt 1.32.0
Propagated dependencies: r-s4vectors@0.48.0 r-knitr@1.50 r-jsonlite@2.0.0 r-iranges@2.44.0 r-htmlwidgets@1.6.4 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-data-table@1.17.8 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/Marlin-Na/TnT
Licenses: AGPL 3
Build system: r
Synopsis: Interactive Visualization for Genomic Features
Description:

This package provides a R interface to the TnT javascript library (https://github.com/ tntvis) to provide interactive and flexible visualization of track-based genomic data.

r-tomoda 1.20.0
Propagated dependencies: r-umap@0.2.10.0 r-summarizedexperiment@1.40.0 r-rtsne@0.17 r-reshape2@1.4.5 r-rcolorbrewer@1.1-3 r-ggrepel@0.9.6 r-ggplot2@4.0.1
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-tracktables 1.44.0
Propagated dependencies: r-xvector@0.50.0 r-xml@3.99-0.20 r-tractor-base@3.5.0 r-stringr@1.6.0 r-rsamtools@2.26.0 r-rcolorbrewer@1.1-3 r-iranges@2.44.0 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/tracktables
Licenses: GPL 3+
Build system: r
Synopsis: Build IGV tracks and HTML reports
Description:

This package provides methods to create complex IGV genome browser sessions and dynamic IGV reports in HTML pages.

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-tofsimsdata 1.38.0
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-topdownr 1.32.0
Propagated dependencies: r-s4vectors@0.48.0 r-psmatch@1.14.0 r-protgenerics@1.42.0 r-mzr@2.44.0 r-msnbase@2.36.0 r-matrix@1.7-4 r-ggplot2@4.0.1 r-biostrings@2.78.0 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://codeberg.org/sgibb/topdownr/
Licenses: GPL 3+
Build system: r
Synopsis: Investigation of Fragmentation Conditions in Top-Down Proteomics
Description:

The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.

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.

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Total results: 68658