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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 search send a patch to ~whereiseveryone/toys@lists.sr.ht adding your channel as an entry in channels.scm.


r-foursynergy 1.0.0
Propagated dependencies: r-yaml@2.3.12 r-txdb-mmusculus-ucsc-mm10-knowngene@3.10.0 r-txdb-hsapiens-ucsc-hg19-knowngene@3.22.1 r-tidyr@1.3.2 r-tibble@3.3.1 r-stringr@1.6.0 r-reshape2@1.4.5 r-org-mm-eg-db@3.23.0 r-org-hs-eg-db@3.23.1 r-magrittr@2.0.5 r-karyoploter@1.38.0 r-jsonlite@2.0.0 r-ggplot2@4.0.3 r-genomicranges@1.64.0 r-genomeinfodb@1.48.0 r-dplyr@1.2.1 r-deseq2@1.52.0 r-bamsignals@1.44.1
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/sophiewind/fourSynergy
Licenses: LGPL 3
Build system: r
Synopsis: Ensemble algorithm for 4C-seq data
Description:

fourSynergy is an ensemble algorithm leveraging synergies among the existing 4C-seq algorithms r3C-seq, peakC, r.4cker and fourSig. It uses a weighted voting approach to perform improved interaction calling. fourSynergy supports also differential interaction calling.

r-flowtrans 1.64.0
Propagated dependencies: r-flowviz@1.76.0 r-flowcore@2.24.0 r-flowclust@3.50.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/flowTrans
Licenses: Artistic License 2.0
Build system: r
Synopsis: Parameter Optimization for Flow Cytometry Data Transformation
Description:

Profile maximum likelihood estimation of parameters for flow cytometry data transformations.

r-frenchfish 1.24.0
Propagated dependencies: r-nhpoisson@3.4 r-mcmcpack@1.7-1
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/frenchFISH
Licenses: Artistic License 2.0
Build system: r
Synopsis: Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections
Description:

FrenchFISH comprises a nuclear volume correction method coupled with two types of Poisson models: either a Poisson model for improved manual spot counting without the need for control probes; or a homogenous Poisson Point Process model for automated spot counting.

r-flagme 1.68.0
Propagated dependencies: r-xcms@4.10.0 r-sparsem@1.84-2 r-mass@7.3-65 r-gplots@3.3.0 r-gcspikelite@1.50.0 r-camera@1.68.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/flagme
Licenses: LGPL 2.0+
Build system: r
Synopsis: Analysis of Metabolomics GC/MS Data
Description:

Fragment-level analysis of gas chromatography-massspectrometry metabolomics data.

r-flowvs 1.44.0
Propagated dependencies: r-flowviz@1.76.0 r-flowstats@4.24.0 r-flowcore@2.24.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/flowVS
Licenses: Artistic License 2.0
Build system: r
Synopsis: Variance stabilization in flow cytometry (and microarrays)
Description:

Per-channel variance stabilization from a collection of flow cytometry samples by Bertlett test for homogeneity of variances. The approach is applicable to microarrays data as well.

r-flowcybar 1.48.0
Propagated dependencies: r-vegan@2.7-3 r-gplots@3.3.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: http://www.ufz.de/index.php?de=16773
Licenses: GPL 2
Build system: r
Synopsis: Analyze flow cytometric data using gate information
Description:

This package provides a package to analyze flow cytometric data using gate information to follow population/community dynamics.

r-frmatools 1.64.0
Propagated dependencies: r-preprocesscore@1.74.0 r-dbi@1.3.0 r-biobase@2.72.0 r-affy@1.90.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: http://bioconductor.org
Licenses: GPL 2+
Build system: r
Synopsis: Frozen RMA Tools
Description:

This package provides tools for advanced use of the frma package.

r-flowspecs 1.26.0
Propagated dependencies: r-zoo@1.8-15 r-reshape2@1.4.5 r-ggplot2@4.0.3 r-flowcore@2.24.0 r-biocparallel@1.46.0 r-biocgenerics@0.58.1 r-biobase@2.72.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/flowSpecs
Licenses: Expat
Build system: r
Synopsis: Tools for processing of high-dimensional cytometry data
Description:

This package is intended to fill the role of conventional cytometry pre-processing software, for spectral decomposition, transformation, visualization and cleanup, and to aid further downstream analyses, such as with DepecheR, by enabling transformation of flowFrames and flowSets to dataframes. Functions for flowCore-compliant automatic 1D-gating/filtering are in the pipe line. The package name has been chosen both as it will deal with spectral cytometry and as it will hopefully give the user a nice pair of spectacles through which to view their data.

r-finfomds 1.2.0
Propagated dependencies: r-phyloseq@1.56.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/soob-kim/FinfoMDS
Licenses: GPL 3
Build system: r
Synopsis: Multidimensional Scaling with F-ratio for microbiome visualization
Description:

F-informed MDS is a new multidimensional scaling-based ordination method that configures data distribution based on the F-statistic (i.e., the ratio of dispersion between groups with shared or differing labels).

r-flowbeads 1.50.0
Propagated dependencies: r-xtable@1.8-8 r-rrcov@1.7-7 r-knitr@1.51 r-flowcore@2.24.0 r-biobase@2.72.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/flowBeads
Licenses: Artistic License 2.0
Build system: r
Synopsis: flowBeads: Analysis of flow bead data
Description:

This package extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalisation.

r-flowclean 1.50.0
Propagated dependencies: r-sfsmisc@1.1-24 r-flowcore@2.24.0 r-changepoint@2.3 r-bit@4.6.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/flowClean
Licenses: Artistic License 2.0
Build system: r
Synopsis: flowClean
Description:

This package provides a quality control tool for flow cytometry data based on compositional data analysis.

r-fdb-ucsc-snp135common-hg19 1.0.0
Propagated dependencies: r-genomicfeatures@1.64.0 r-annotationdbi@1.74.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/FDb.UCSC.snp135common.hg19
Licenses: Artistic License 2.0
Build system: r
Synopsis: UCSC common SNPs track for dbSNP build 135
Description:

makeFeatureDbFromUCSC cannot cope with this track, hence a package.

r-fitcons-ucsc-hg19 3.7.1
Propagated dependencies: r-s4vectors@0.50.1 r-iranges@2.46.0 r-genomicscores@2.24.0 r-genomicranges@1.64.0 r-genomeinfodb@1.48.0 r-bsgenome@1.80.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/fitCons.UCSC.hg19
Licenses: Artistic License 2.0
Build system: r
Synopsis: UCSC fitCons fitness consequences scores for hg19
Description:

Store UCSC fitCons fitness consequences scores version 1.01 for the human genome (hg19).

r-fragmentomics 1.0.0
Propagated dependencies: r-variantannotation@1.58.0 r-tidyr@1.3.2 r-tibble@3.3.1 r-stringr@1.6.0 r-scales@1.4.0 r-s4vectors@0.50.1 r-rsamtools@2.28.0 r-rlang@1.2.0 r-readr@2.2.0 r-rcolorbrewer@1.1-3 r-purrr@1.2.2 r-iranges@2.46.0 r-ggseqlogo@0.2.2 r-ggplot2@4.0.3 r-ggh4x@0.3.1 r-genomicranges@1.64.0 r-genomeinfodb@1.48.0 r-future-apply@1.20.2 r-future@1.70.0 r-dplyr@1.2.1 r-data-table@1.18.4 r-biostrings@2.80.1
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/ElsaB-Lab/fRagmentomics
Licenses: GPL 3+
Build system: r
Synopsis: Extract Fragmentomics Features and Mutational Status
Description:

This package provides a user-friendly R package that enables the characterization of each cfDNA fragment overlapping one or multiple mutations of interest, starting from a sequencing file containing aligned reads (BAM file). fRagmentomics supports multiple mutation input formats (e.g., VCF, TSV, or string "chr:pos:ref:alt" representation), accommodates one-based and zero-based genomic conventions, handles mutation representation ambiguities, and accepts any reference file and species in FASTA format. For each cfDNA fragment, fRagmentomics outputs its size, its 3 and 5 sequences, and its mutational status. Optionally, when users set apply_bcftools_norm = TRUE, fRagmentomics invokes the external command-line tool bcftools norm to left-align and normalize variants. If bcftools is not found on the system PATH while this option is enabled, the function errors. The package does not install external software; see the INSTALL file for per-OS instructions.

r-fission 1.32.0
Propagated dependencies: r-summarizedexperiment@1.42.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/fission
Licenses: LGPL 2.0+
Build system: r
Synopsis: RangedSummarizedExperiment for time course RNA-Seq of fission yeast in response to stress, by Leong et al., Nat Commun 2014
Description:

This package provides a RangedSummarizedExperiment object of read counts in genes for a time course RNA-Seq experiment of fission yeast (Schizosaccharomyces pombe) in response to oxidative stress (1M sorbitol treatment) at 0, 15, 30, 60, 120 and 180 mins. The samples are further divided between a wild-type group and a group with deletion of atf21. The read count matrix was prepared and provided by the author of the study: Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ. "A global non-coding RNA system modulates fission yeast protein levels in response to stress". Nat Commun 2014 May 23;5:3947. PMID: 24853205. GEO: GSE56761.

r-factdesign 1.88.0
Propagated dependencies: r-biobase@2.72.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/factDesign
Licenses: LGPL 2.0+
Build system: r
Synopsis: Factorial designed microarray experiment analysis
Description:

This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection.

r-fella 1.32.0
Propagated dependencies: r-plyr@1.8.9 r-matrix@1.7-5 r-keggrest@1.52.0 r-igraph@2.3.1
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/FELLA
Licenses: GPL 3
Build system: r
Synopsis: Interpretation and enrichment for metabolomics data
Description:

Enrichment of metabolomics data using KEGG entries. Given a set of affected compounds, FELLA suggests affected reactions, enzymes, modules and pathways using label propagation in a knowledge model network. The resulting subnetwork can be visualised and exported.

r-fdb-infiniummethylation-hg18 2.2.0
Propagated dependencies: r-txdb-hsapiens-ucsc-hg18-knowngene@3.2.2 r-org-hs-eg-db@3.23.1 r-genomicfeatures@1.64.0 r-biostrings@2.80.1 r-annotationdbi@1.74.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/FDb.InfiniumMethylation.hg18
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for Illumina Infinium DNA methylation probes
Description:

Compiled HumanMethylation27 and HumanMethylation450 annotations.

r-flowpeaks 1.58.0
Dependencies: gsl@2.8
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/flowPeaks
Licenses: FSDG-compatible
Build system: r
Synopsis: An R package for flow data clustering
Description:

This package provides a fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.

r-flowtime 1.36.0
Propagated dependencies: r-tibble@3.3.1 r-rlang@1.2.0 r-plyr@1.8.9 r-magrittr@2.0.5 r-flowcore@2.24.0 r-dplyr@1.2.1
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/flowTime
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation and analysis of biological dynamical systems using flow cytometry
Description:

This package facilitates analysis of both timecourse and steady state flow cytometry experiments. This package was originially developed for quantifying the function of gene regulatory networks in yeast (strain W303) expressing fluorescent reporter proteins using BD Accuri C6 and SORP cytometers. However, the functions are for the most part general and may be adapted for analysis of other organisms using other flow cytometers. Functions in this package facilitate the annotation of flow cytometry data with experimental metadata, as often required for publication and general ease-of-reuse. Functions for creating, saving and loading gate sets are also included. In the past, we have typically generated summary statistics for each flowset for each timepoint and then annotated and analyzed these summary statistics. This method loses a great deal of the power that comes from the large amounts of individual cell data generated in flow cytometry, by essentially collapsing this data into a bulk measurement after subsetting. In addition to these summary functions, this package also contains functions to facilitate annotation and analysis of steady-state or time-lapse data utilizing all of the data collected from the thousands of individual cells in each sample.

r-fenr 1.10.0
Propagated dependencies: r-tidyselect@1.2.1 r-tidyr@1.3.2 r-tibble@3.3.1 r-stringr@1.6.0 r-shiny@1.13.0 r-rvest@1.0.5 r-rlang@1.2.0 r-readr@2.2.0 r-purrr@1.2.2 r-progress@1.2.3 r-httr2@1.2.2 r-ggplot2@4.0.3 r-dplyr@1.2.1 r-biocfilecache@3.2.0 r-assertthat@0.2.1
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/bartongroup/fenr
Licenses: Expat
Build system: r
Synopsis: Fast functional enrichment for interactive applications
Description:

Perform fast functional enrichment on feature lists (like genes or proteins) using the hypergeometric distribution. Tailored for speed, this package is ideal for interactive platforms such as Shiny. It supports the retrieval of functional data from sources like GO, KEGG, Reactome, Bioplanet and WikiPathways. By downloading and preparing data first, it allows for rapid successive tests on various feature selections without the need for repetitive, time-consuming preparatory steps typical of other packages.

r-frgepistasis 1.48.0
Propagated dependencies: r-mass@7.3-65 r-fda@6.3.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/FRGEpistasis
Licenses: GPL 2
Build system: r
Synopsis: Epistasis Analysis for Quantitative Traits by Functional Regression Model
Description:

This package provides a Tool for Epistasis Analysis Based on Functional Regression Model.

r-frmaexampledata 1.48.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/frmaExampleData
Licenses: GPL 2+
Build system: r
Synopsis: Frma Example Data
Description:

Data files used by the examples in frma and frmaTools packages.

r-fedup 1.19.0
Propagated dependencies: r-tibble@3.3.1 r-rcy3@2.32.0 r-rcolorbrewer@1.1-3 r-openxlsx@4.2.8.1 r-ggthemes@5.2.0 r-ggplot2@4.0.3 r-forcats@1.0.1 r-dplyr@1.2.1 r-data-table@1.18.4
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/rosscm/fedup
Licenses: Expat
Build system: r
Synopsis: Fisher's Test for Enrichment and Depletion of User-Defined Pathways
Description:

An R package that tests for enrichment and depletion of user-defined pathways using a Fisher's exact test. The method is designed for versatile pathway annotation formats (eg. gmt, txt, xlsx) to allow the user to run pathway analysis on custom annotations. This package is also integrated with Cytoscape to provide network-based pathway visualization that enhances the interpretability of the results.

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Total packages: 3017