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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:

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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-fission 1.30.0
Propagated dependencies: r-summarizedexperiment@1.40.0
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-funtoonorm 1.34.0
Propagated dependencies: r-pls@2.8-5 r-minfi@1.56.0 r-matrixstats@1.5.0 r-illuminahumanmethylation450kmanifest@0.4.0 r-illuminahumanmethylation450kanno-ilmn12-hg19@0.6.1 r-genomeinfodb@1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/funtooNorm
Licenses: GPL 3
Build system: r
Synopsis: Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit
Description:

This package provides a function to normalize Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell type.

r-fastreer 2.0.0
Dependencies: openjdk@25
Propagated dependencies: r-stringr@1.6.0 r-rjava@1.0-11 r-r-utils@2.13.0 r-dynamictreecut@1.63-1 r-data-table@1.17.8 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/gkanogiannis/fastreeR
Licenses: GPL 3
Build system: r
Synopsis: Phylogenetic, Distance and Other Calculations on VCF and Fasta Files
Description:

Calculate distances, build phylogenetic trees or perform hierarchical clustering between the samples of a VCF or FASTA file. Functions are implemented in Java-11 and called via rJava. Parallel implementation that operates directly on the VCF or FASTA file for fast execution.

r-finfomds 1.0.0
Propagated dependencies: r-phyloseq@1.54.0
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-frenchfish 1.22.0
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-flowbeads 1.48.0
Propagated dependencies: r-xtable@1.8-4 r-rrcov@1.7-7 r-knitr@1.50 r-flowcore@2.22.0 r-biobase@2.70.0
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-fobitools 1.18.0
Propagated dependencies: r-vroom@1.6.6 r-tidyr@1.3.1 r-tidygraph@1.3.1 r-tictoc@1.2.1 r-textclean@0.9.3 r-stringr@1.6.0 r-recordlinkage@0.4-12.6 r-purrr@1.2.0 r-ontologyindex@2.12 r-magrittr@2.0.4 r-ggraph@2.2.2 r-ggplot2@4.0.1 r-fgsea@1.36.0 r-dplyr@1.1.4 r-crayon@1.5.3 r-clisymbols@1.2.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/pcastellanoescuder/fobitools/
Licenses: GPL 3
Build system: r
Synopsis: Tools for Manipulating the FOBI Ontology
Description:

This package provides a set of tools for interacting with the Food-Biomarker Ontology (FOBI). A collection of basic manipulation tools for biological significance analysis, graphs, and text mining strategies for annotating nutritional data.

r-flowploidydata 1.36.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/flowPloidyData
Licenses: GPL 3
Build system: r
Synopsis: Example Flow Cytometry Data
Description:

This package provides a collection of raw flow cytometry data for use in vignettes for the flowPloidy package.

r-filterffpe 1.20.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-foreach@1.5.2 r-doparallel@1.0.17
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/FilterFFPE
Licenses: LGPL 3
Build system: r
Synopsis: FFPE Artificial Chimeric Read Filter for NGS data
Description:

This package finds and filters artificial chimeric reads specifically generated in next-generation sequencing (NGS) process of formalin-fixed paraffin-embedded (FFPE) tissues. These artificial chimeric reads can lead to a large number of false positive structural variation (SV) calls. The required input is an indexed BAM file of a FFPE sample.

r-fdb-ucsc-snp137common-hg19 1.0.0
Propagated dependencies: r-genomicfeatures@1.62.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/FDb.UCSC.snp137common.hg19
Licenses: Artistic License 2.0
Build system: r
Synopsis: UCSC common SNPs track for dbSNP build 137
Description:

makeFeatureDbFromUCSC cannot cope with this track, hence a package.

r-flowsorted-cordblood-450k 1.38.0
Propagated dependencies: r-minfi@1.56.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/FlowSorted.CordBlood.450k
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina 450k data on sorted cord blood cells
Description:

Raw data objects to be used for cord blood cell proportion estimation in minfi.

r-flowdensity 1.44.0
Dependencies: libxml2@2.14.6
Propagated dependencies: r-polyclip@1.10-7 r-gplots@3.2.0 r-flowviz@1.74.0 r-flowcore@2.22.0 r-car@3.1-3
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/flowDensity
Licenses: Artistic License 2.0
Build system: r
Synopsis: Sequential Flow Cytometry Data Gating
Description:

This package provides tools for automated sequential gating analogous to the manual gating strategy based on the density of the data.

r-ffpe 1.54.0
Propagated dependencies: r-ttr@0.24.4 r-sfsmisc@1.1-23 r-methylumi@2.56.0 r-lumi@2.62.0 r-biocgenerics@0.56.0 r-biobase@2.70.0 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/ffpe
Licenses: FSDG-compatible
Build system: r
Synopsis: Quality assessment and control for FFPE microarray expression data
Description:

Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).

r-fletcher2013b 1.46.0
Propagated dependencies: r-rtn@2.34.0 r-reder@3.6.0 r-rcolorbrewer@1.1-3 r-igraph@2.2.1 r-fletcher2013a@1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: http://dx.doi.org/10.1038/ncomms3464
Licenses: GPL 2+
Build system: r
Synopsis: Master regulators of FGFR2 signalling and breast cancer risk
Description:

This package reproduces the systems biology analysis for the data in package Fletcher2013a using RTN.

r-flowgraph 1.18.0
Propagated dependencies: r-visnetwork@2.1.4 r-stringr@1.6.0 r-stringi@1.8.7 r-rdpack@2.6.4 r-purrr@1.2.0 r-matrixstats@1.5.0 r-matrix@1.7-4 r-igraph@2.2.1 r-htmlwidgets@1.6.4 r-gridextra@2.3 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-ggiraph@0.9.2 r-future@1.68.0 r-furrr@0.3.1 r-effsize@0.8.1 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/aya49/flowGraph
Licenses: Artistic License 2.0
Build system: r
Synopsis: Identifying differential cell populations in flow cytometry data accounting for marker frequency
Description:

Identifies maximal differential cell populations in flow cytometry data taking into account dependencies between cell populations; flowGraph calculates and plots SpecEnr abundance scores given cell population cell counts.

r-flowsorted-cordbloodcombined-450k 1.26.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-minfi@1.56.0 r-illuminahumanmethylationepicanno-ilm10b4-hg19@0.6.0 r-illuminahumanmethylation450kanno-ilmn12-hg19@0.6.1 r-experimenthub@3.0.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k
Licenses: GPL 3
Build system: r
Synopsis: Illumina 450k/EPIC data on FACS and MACS umbilical blood cells
Description:

Raw data objects to be used for umbilical cord blood cell proportion estimation in minfi and similar packages. The FlowSorted.CordBloodCombined.450k object is based in samples assayed by Bakulski et al, Gervin et al., de Goede et al., and Lin et al.

r-fibroeset 1.52.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/fibroEset
Licenses: LGPL 2.0+
Build system: r
Synopsis: exprSet for Karaman et al. (2003) fibroblasts data
Description:

exprSet for Karaman et al. (2003) human, bonobo and gorilla fibroblasts data.

r-fletcher2013a 1.46.0
Propagated dependencies: r-venndiagram@1.7.3 r-limma@3.66.0 r-gplots@3.2.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: http://dx.doi.org/10.1038/ncomms3464
Licenses: GPL 2+
Build system: r
Synopsis: Gene expression data from breast cancer cells under FGFR2 signalling perturbation
Description:

The package Fletcher2013a contains time-course gene expression data from MCF-7 cells treated under different experimental systems in order to perturb FGFR2 signalling. The data comes from Fletcher et al. (Nature Comms 4:2464, 2013) where further details about the background and the experimental design of the study can be found.

r-featseekr 1.10.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-pracma@2.4.6 r-pheatmap@1.0.13 r-mass@7.3-65
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/tcapraz/FeatSeekR
Licenses: GPL 3
Build system: r
Synopsis: FeatSeekR an R package for unsupervised feature selection
Description:

FeatSeekR performs unsupervised feature selection using replicated measurements. It iteratively selects features with the highest reproducibility across replicates, after projecting out those dimensions from the data that are spanned by the previously selected features. The selected a set of features has a high replicate reproducibility and a high degree of uniqueness.

r-ffpeexampledata 1.48.0
Propagated dependencies: r-lumi@2.62.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/ffpeExampleData
Licenses: FSDG-compatible
Build system: r
Synopsis: Illumina DASL example microarray data
Description:

This package provides a subset of GSE17565 (April et al. 2009) containing 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with a dilution series in technical duplicate.

r-flowsorted-cordbloodnorway-450k 1.36.0
Propagated dependencies: r-minfi@1.56.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bitbucket.com/kasperdanielhansen/Illumina_CordBlood
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina HumanMethylation data on sorted cord blood cell populations
Description:

Raw data objects for the Illumina 450k DNA methylation microarrays, for cell type composition estimation.

r-fdb-infiniummethylation-hg18 2.2.0
Propagated dependencies: r-txdb-hsapiens-ucsc-hg18-knowngene@3.2.2 r-org-hs-eg-db@3.22.0 r-genomicfeatures@1.62.0 r-biostrings@2.78.0 r-annotationdbi@1.72.0
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-frgepistasis 1.46.0
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-fdb-ucsc-snp135common-hg19 1.0.0
Propagated dependencies: r-genomicfeatures@1.62.0 r-annotationdbi@1.72.0
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.

Total results: 2909