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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.

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r-bioassayr 1.48.0
Propagated dependencies: r-biocgenerics@0.56.0 r-chemminer@3.62.0 r-dbi@1.2.3 r-matrix@1.7-4 r-rjson@0.2.23 r-rsqlite@2.4.4 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/girke-lab/bioassayR
Licenses: Artistic License 2.0
Build system: r
Synopsis: Cross-target analysis of small molecule bioactivity
Description:

bioassayR is a computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses of both public and custom bioassays, generation of high throughput screening fingerprints (HTSFPs), and an optional preloaded database that provides access to a substantial portion of publicly available bioactivity data.

r-cigarillo 1.0.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-iranges@2.44.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/cigarillo
Licenses: Artistic License 2.0
Build system: r
Synopsis: Efficient manipulation of CIGAR strings
Description:

CIGAR stands for Concise Idiosyncratic Gapped Alignment Report. CIGAR strings are found in the BAM files produced by most aligners and in the AIRR-formatted output produced by IgBLAST. The cigarillo package provides functions to parse and inspect CIGAR strings, trim them, turn them into ranges of positions relative to the "query space" or "reference space", and project positions or sequences from one space to the other. Note that these operations are low-level operations that the user rarely needs to perform directly. More typically, they are performed behind the scene by higher-level functionality implemented in other packages like Bioconductor packages GenomicAlignments and igblastr.

r-triform 1.29.0
Propagated dependencies: r-biocgenerics@0.56.0 r-iranges@2.44.0 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/triform/
Licenses: GPL 2
Build system: r
Synopsis: Find enriched regions in transcription factor ChIP-sequencing data
Description:

The Triform algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics.

r-aucell 1.32.0
Propagated dependencies: r-biocgenerics@0.56.0 r-data-table@1.17.8 r-delayedarray@0.36.0 r-delayedmatrixstats@1.32.0 r-gseabase@1.72.0 r-matrix@1.7-4 r-mixtools@2.0.0.1 r-r-utils@2.13.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AUCell/
Licenses: GPL 3
Build system: r
Synopsis: Analysis of gene set activity in single-cell RNA-seq data
Description:

AUCell identifies cells with active gene sets (e.g. signatures, gene modules, etc) in single-cell RNA-seq data. AUCell uses the Area Under the Curve (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.

r-biobroom 1.42.0
Propagated dependencies: r-biobase@2.70.0 r-broom@1.0.10 r-dplyr@1.1.4 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/StoreyLab/biobroom
Licenses: LGPL 3+
Build system: r
Synopsis: Turn Bioconductor objects into tidy data frames
Description:

This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.

r-bumphunter 1.52.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biocgenerics@0.56.0 r-dorng@1.8.6.2 r-foreach@1.5.2 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-iterators@1.0.14 r-limma@3.66.0 r-locfit@1.5-9.12 r-matrixstats@1.5.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ririzarr/bumphunter
Licenses: Artistic License 2.0
Build system: r
Synopsis: Find bumps in genomic data
Description:

This package provides tools for finding bumps in genomic data in order to identify differentially methylated regions in epigenetic epidemiology studies.

r-deconvr 1.16.0
Propagated dependencies: r-assertthat@0.2.1 r-biocgenerics@0.56.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-e1071@1.7-16 r-foreach@1.5.2 r-genomicranges@1.62.0 r-iranges@2.44.0 r-magrittr@2.0.4 r-mass@7.3-65 r-matrixstats@1.5.0 r-methylkit@1.36.0 r-minfi@1.56.0 r-nnls@1.6 r-quadprog@1.5-8 r-rsq@2.7 r-s4vectors@0.48.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/BIMSBbioinfo/deconvR
Licenses: Artistic License 2.0
Build system: r
Synopsis: Simulation and deconvolution of omic profiles
Description:

This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types. The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally, we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.

r-degreport 1.46.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-broom@1.0.10 r-circlize@0.4.16 r-cluster@2.1.8.1 r-complexheatmap@2.26.0 r-consensusclusterplus@1.74.0 r-cowplot@1.2.0 r-dendextend@1.19.1 r-deseq2@1.50.2 r-dplyr@1.1.4 r-edger@4.8.0 r-ggdendro@0.2.0 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-knitr@1.50 r-logging@0.10-108 r-magrittr@2.0.4 r-psych@2.5.6 r-rcolorbrewer@1.1-3 r-reshape@0.8.10 r-rlang@1.1.6 r-s4vectors@0.48.0 r-scales@1.4.0 r-stringi@1.8.7 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-tibble@3.3.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://lpantano.github.io/DEGreport/
Licenses: Expat
Build system: r
Synopsis: Report of DEG analysis
Description:

This is a package for creating na HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.

r-quasr 1.50.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-biostrings@2.78.0 r-bsgenome@1.78.0 r-genomicfeatures@1.62.0 r-genomicfiles@1.46.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-rbowtie@1.50.0 r-rhtslib@3.6.0 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-shortread@1.68.0 r-txdbmaker@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/QuasR/
Licenses: GPL 2
Build system: r
Synopsis: Quantify and annotate short reads in R
Description:

This package provides a framework for the quantification and analysis of short genomic reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.

r-affycoretools 1.82.0
Propagated dependencies: r-affy@1.88.0 r-annotationdbi@1.72.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-dbi@1.2.3 r-edger@4.8.0 r-gcrma@2.82.0 r-ggplot2@4.0.1 r-glimma@2.20.0 r-gostats@2.76.0 r-gplots@3.2.0 r-hwriter@1.3.2.1 r-lattice@0.22-7 r-limma@3.66.0 r-oligoclasses@1.72.0 r-reportingtools@2.50.0 r-rsqlite@2.4.4 r-s4vectors@0.48.0 r-xtable@1.8-4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/affycoretools/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Functions for analyses with Affymetrix GeneChips
Description:

This package provides various wrapper functions that have been written to streamline the more common analyses that a Biostatistician might see.

r-structstrings 1.26.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-crayon@1.5.3 r-iranges@2.44.0 r-s4vectors@0.48.0 r-stringi@1.8.7 r-stringr@1.6.0 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/FelixErnst/Structstrings
Licenses: Artistic License 2.0
Build system: r
Synopsis: Implementation of the dot bracket annotations with Biostrings
Description:

The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.

r-a4preproc 1.58.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/a4Preproc/
Licenses: GPL 3
Build system: r
Synopsis: Automated Affymetrix array analysis preprocessing package
Description:

This is a package for the automated analysis of Affymetrix arrays. It is used for preprocessing the arrays.

r-agdex 1.58.0
Propagated dependencies: r-biobase@2.70.0 r-gseabase@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AGDEX
Licenses: GPL 2+
Build system: r
Synopsis: Evaluate agreement of differential expression for cross-species genomics
Description:

The objective of AGDEX is to evaluate whether the results of a pair of two-group differential expression analysis comparisons show a level of agreement that is greater than expected if the group labels for each two-group comparison are randomly assigned. The agreement is evaluated for the entire transcriptome and (optionally) for a collection of pre-defined gene-sets. Additionally, the procedure performs permutation-based differential expression and meta analysis at both gene and gene-set levels of the data from each experiment.

r-widgettools 1.88.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/widgetTools/
Licenses: LGPL 3+
Build system: r
Synopsis: Tools for creating interactive tcltk widgets
Description:

This package contains tools to support the construction of tcltk widgets in R.

r-enhancedvolcano 1.26.0
Propagated dependencies: r-ggplot2@4.0.1 r-ggrepel@0.9.6
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/kevinblighe/EnhancedVolcano
Licenses: GPL 3
Build system: r
Synopsis: Publication-ready volcano plots with enhanced coloring and labeling
Description:

Volcano plots represent a useful way to visualise the results of differential expression analyses. This package provides a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many point labels in the plot window as possible, thus avoiding clogging up the plot with labels that could not otherwise have been read. Other functionality allows the user to identify up to 4 different types of attributes in the same plot space via color, shape, size, and shade parameter configurations.

r-seqarray 1.50.0
Propagated dependencies: r-biostrings@2.78.0 r-digest@0.6.39 r-gdsfmt@1.46.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/zhengxwen/SeqArray
Licenses: GPL 3
Build system: r
Synopsis: Data management of large-scale whole-genome sequence variant calls
Description:

This package supports data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.

r-annotatr 1.36.0
Propagated dependencies: r-annotationdbi@1.72.0 r-annotationhub@4.0.0 r-dplyr@1.1.4 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-readr@2.1.6 r-regioner@1.42.0 r-reshape2@1.4.5 r-rlang@1.1.6 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/annotatr/
Licenses: GPL 3
Build system: r
Synopsis: Annotation of genomic regions to genomic annotations
Description:

Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.

r-stringdb 2.22.0
Propagated dependencies: r-gplots@3.2.0 r-hash@2.2.6.3 r-httr@1.4.7 r-igraph@2.2.1 r-plotrix@3.8-13 r-plyr@1.8.9 r-png@0.1-8 r-rcolorbrewer@1.1-3 r-sqldf@0.4-11
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://git.bioconductor.org/packages/STRINGdb
Licenses: GPL 2
Build system: r
Synopsis: Search tool for the retrieval of interacting proteins database
Description:

The STRINGdb package provides an R interface to the STRING protein-protein interactions database. STRING is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations. Each interaction is associated with a combined confidence score that integrates the various evidences.

r-coregx 2.14.0
Propagated dependencies: r-bench@1.1.4 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-bumpymatrix@1.18.0 r-checkmate@2.3.3 r-crayon@1.5.3 r-data-table@1.17.8 r-glue@1.8.0 r-lsa@0.73.3 r-matrixgenerics@1.22.0 r-multiassayexperiment@1.36.1 r-piano@2.26.0 r-rlang@1.1.6 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/CoreGx
Licenses: GPL 3+
Build system: r
Synopsis: Classes and functions to serve as the basis for other Gx packages
Description:

This package provides a collection of functions and classes which serve as the foundation for packages such as PharmacoGx and RadioGx. It was created to abstract shared functionality to increase ease of maintainability and reduce code repetition in current and future Gx suite programs. Major features include a CoreSet class, from which RadioSet and PharmacoSet are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating AUC or SF are included.

r-gwascat 2.42.0
Propagated dependencies: r-annotationdbi@1.72.0 r-annotationhub@4.0.0 r-biocfilecache@3.0.0 r-biostrings@2.78.0 r-data-table@1.17.8 r-genomeinfodb@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-readr@2.1.6 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-snpstats@1.60.0 r-tibble@3.3.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/gwascat
Licenses: Artistic License 2.0
Build system: r
Synopsis: Tools for data in the EMBL-EBI GWAS catalog
Description:

This package provides tools for representing and modeling data in the EMBL-EBI GWAS catalog.

r-screpertoire 2.5.8
Propagated dependencies: r-dplyr@1.1.4 r-evmix@2.12 r-ggalluvial@0.12.5 r-ggdendro@0.2.0 r-ggplot2@4.0.1 r-ggraph@2.2.2 r-igraph@2.2.1 r-immapex@1.4.0 r-inext@3.0.2 r-lifecycle@1.0.4 r-matrix@1.7-4 r-purrr@1.2.0 r-quantreg@6.1 r-rcpp@1.1.0 r-rjson@0.2.23 r-rlang@1.1.6 r-s4vectors@0.48.0 r-seuratobject@5.2.0 r-singlecellexperiment@1.32.0 r-summarizedexperiment@1.40.0 r-tidygraph@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/scRepertoire
Licenses: GPL 2
Build system: r
Synopsis: Toolkit for single-cell immune receptor profiling
Description:

The scRepertoire package was built to process data derived from the 10x Genomics Chromium Immune Profiling for both TCR and Ig enrichment workflows and subsequently interacts with the popular Seurat and SingleCellExperiment R packages. It also allows for general analysis of single-cell clonotype information without the use of expression information. The package functions as a wrapper for Startrac and powerTCR R packages.

r-htscluster 2.0.11
Propagated dependencies: r-capushe@1.1.3 r-edger@4.8.0 r-plotrix@3.8-13
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/web/packages/HTSCluster
Licenses: GPL 3+
Build system: r
Synopsis: Clustering high-throughput transcriptome sequencing (HTS) data
Description:

This package provides a Poisson mixture model is implemented to cluster genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter estimation is performed using either the EM or CEM algorithm, and the slope heuristics are used for model selection (i.e., to choose the number of clusters).

r-infercnv 1.26.0
Dependencies: python@3.11.14
Propagated dependencies: r-ape@5.8-1 r-argparse@2.3.1 r-biocgenerics@0.56.0 r-catools@1.18.3 r-coda@0.19-4.1 r-coin@1.4-3 r-digest@0.6.39 r-doparallel@1.0.17 r-dplyr@1.1.4 r-edger@4.8.0 r-fastcluster@1.3.0 r-fitdistrplus@1.2-4 r-foreach@1.5.2 r-futile-logger@1.4.3 r-future@1.68.0 r-ggplot2@4.0.1 r-gplots@3.2.0 r-gridextra@2.3 r-hiddenmarkov@1.8-14 r-igraph@2.2.1 r-matrix@1.7-4 r-paralleldist@0.2.7 r-phyclust@0.1-34 r-rann@2.6.2 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-rjags@4-17 r-seurat@5.3.1 r-singlecellexperiment@1.32.0 r-summarizedexperiment@1.40.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/broadinstitute/inferCNV/wiki
Licenses: Modified BSD
Build system: r
Synopsis: Infer copy number variation from single-cell RNA-Seq data
Description:

InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence for somatic large-scale chromosomal copy number alterations, such as gains or deletions of entire chromosomes or large segments of chromosomes. This is done by exploring expression intensity of genes across positions of a tumor genome in comparison to a set of reference "normal" cells. A heatmap is generated illustrating the relative expression intensities across each chromosome, and it often becomes readily apparent as to which regions of the tumor genome are over-abundant or less-abundant as compared to that of normal cells.

r-a4base 1.58.0
Propagated dependencies: r-a4core@1.58.0 r-a4preproc@1.58.0 r-annaffy@1.82.0 r-biobase@2.70.0 r-genefilter@1.92.0 r-glmnet@4.1-10 r-gplots@3.2.0 r-limma@3.66.0 r-mpm@1.0-23 r-multtest@2.66.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/a4Base/
Licenses: GPL 3
Build system: r
Synopsis: Automated Affymetrix array analysis base package
Description:

This package provides basic features for the automated analysis of Affymetrix arrays.

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Total results: 69112