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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-flowsorted-dlpfc-450k 1.48.0
Propagated dependencies: r-minfi@1.58.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/FlowSorted.DLPFC.450k
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina HumanMethylation data on sorted frontal cortex cell populations
Description:

Raw data objects for the Illumina 450k DNA methylation microarrays.

r-ffpe 1.56.0
Propagated dependencies: r-ttr@0.24.4 r-sfsmisc@1.1-24 r-methylumi@2.58.0 r-lumi@2.64.0 r-biocgenerics@0.58.1 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: 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-flowfp 1.70.0
Propagated dependencies: r-flowviz@1.76.0 r-flowcore@2.24.0 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/flowFP
Licenses: Artistic License 2.0
Build system: r
Synopsis: Fingerprinting for Flow Cytometry
Description:

Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.

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-fastliquidassociation 1.48.0
Propagated dependencies: r-wgcna@1.74 r-preprocesscore@1.74.0 r-liquidassociation@1.66.0 r-impute@1.86.0 r-hmisc@5.2-5 r-doparallel@1.0.17
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/fastLiquidAssociation
Licenses: GPL 2
Build system: r
Synopsis: functions for genome-wide application of Liquid Association
Description:

This package extends the function of the LiquidAssociation package for genome-wide application. It integrates a screening method into the LA analysis to reduce the number of triplets to be examined for a high LA value and provides code for use in subsequent significance analyses.

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-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-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-fraser 2.8.0
Propagated dependencies: r-vgam@1.1-14 r-txdbmaker@1.8.0 r-tibble@3.3.1 r-summarizedexperiment@1.42.0 r-s4vectors@0.50.1 r-rsubread@2.26.0 r-rsamtools@2.28.0 r-rmtstat@0.3.1 r-rhdf5@2.56.0 r-rcpparmadillo@15.2.6-1 r-rcpp@1.1.1-1.1 r-rcolorbrewer@1.1-3 r-r-utils@2.13.0 r-prroc@1.4 r-pracma@2.4.6 r-plotly@4.12.0 r-pheatmap@1.0.13 r-pcamethods@2.4.0 r-outrider@1.30.0 r-matrixstats@1.5.0 r-iranges@2.46.0 r-hdf5array@1.40.0 r-ggrepel@0.9.8 r-ggplot2@4.0.3 r-genomicranges@1.64.0 r-genomicfeatures@1.64.0 r-genomicalignments@1.48.0 r-genomeinfodb@1.48.0 r-generics@0.1.4 r-extradistr@1.10.0.4 r-delayedmatrixstats@1.34.0 r-delayedarray@0.38.1 r-data-table@1.18.4 r-cowplot@1.2.0 r-bsgenome@1.80.0 r-biomart@2.68.0 r-biocparallel@1.46.0 r-biocgenerics@0.58.1 r-biobase@2.72.0 r-bbmisc@1.13.1 r-annotationdbi@1.74.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/gagneurlab/FRASER
Licenses: FSDG-compatible
Build system: r
Synopsis: Find RAre Splicing Events in RNA-Seq Data
Description:

Detection of rare aberrant splicing events in transcriptome profiles. Read count ratio expectations are modeled by an autoencoder to control for confounding factors in the data. Given these expectations, the ratios are assumed to follow a beta-binomial distribution with a junction specific dispersion. Outlier events are then identified as read-count ratios that deviate significantly from this distribution. FRASER is able to detect alternative splicing, but also intron retention. The package aims to support diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects.

r-fccac 1.38.0
Propagated dependencies: r-s4vectors@0.50.1 r-rcolorbrewer@1.1-3 r-iranges@2.46.0 r-ggplot2@4.0.3 r-genomicranges@1.64.0 r-genomation@1.44.0 r-fda@6.3.0 r-complexheatmap@2.28.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/pmb59/fCCAC
Licenses: Artistic License 2.0
Build system: r
Synopsis: functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
Description:

Computational evaluation of variability across DNA or RNA sequencing datasets is a crucial step in genomics, as it allows both to evaluate reproducibility of replicates, and to compare different datasets to identify potential correlations. fCCAC applies functional Canonical Correlation Analysis to allow the assessment of: (i) reproducibility of biological or technical replicates, analyzing their shared covariance in higher order components; and (ii) the associations between different datasets. fCCAC represents a more sophisticated approach that complements Pearson correlation of genomic coverage.

r-fastqcleaner 1.30.0
Propagated dependencies: r-shortread@1.70.0 r-shinybs@0.65.0 r-shiny@1.13.0 r-s4vectors@0.50.1 r-rcpp@1.1.1-1.1 r-iranges@2.46.0 r-htmltools@0.5.9 r-dt@0.34.0 r-biostrings@2.80.1
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/FastqCleaner
Licenses: Expat
Build system: r
Synopsis: Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files
Description:

An interactive web application for quality control, filtering and trimming of FASTQ files. This user-friendly tool combines a pipeline for data processing based on Biostrings and ShortRead infrastructure, with a cutting-edge visual environment. Single-Read and Paired-End files can be locally processed. Diagnostic interactive plots (CG content, per-base sequence quality, etc.) are provided for both the input and output files.

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-fdrame 1.84.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/fdrame
Licenses: GPL 2+
Build system: r
Synopsis: FDR adjustments of Microarray Experiments (FDR-AME)
Description:

This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma.

r-findit2 1.18.0
Propagated dependencies: r-withr@3.0.2 r-tidyr@1.3.2 r-tibble@3.3.1 r-summarizedexperiment@1.42.0 r-stringr@1.6.0 r-seqinfo@1.2.0 r-s4vectors@0.50.1 r-rtracklayer@1.72.0 r-rlang@1.2.0 r-qvalue@2.44.0 r-purrr@1.2.2 r-progress@1.2.3 r-patchwork@1.3.2 r-multiassayexperiment@1.38.0 r-iranges@2.46.0 r-glmnet@5.0 r-ggrepel@0.9.8 r-ggplot2@4.0.3 r-genomicranges@1.64.0 r-genomicfeatures@1.64.0 r-dplyr@1.2.1 r-biocparallel@1.46.0 r-biocgenerics@0.58.1
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/shangguandong1996/FindIT2
Licenses: Artistic License 2.0
Build system: r
Synopsis: find influential TF and Target based on multi-omics data
Description:

This package implements functions to find influential TF and target based on different input type. It have five module: Multi-peak multi-gene annotaion(mmPeakAnno module), Calculate regulation potential(calcRP module), Find influential Target based on ChIP-Seq and RNA-Seq data(Find influential Target module), Find influential TF based on different input(Find influential TF module), Calculate peak-gene or peak-peak correlation(peakGeneCor module). And there are also some other useful function like integrate different source information, calculate jaccard similarity for your TF.

r-fis 1.40.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/FIs
Licenses: GPL 3
Build system: r
Synopsis: Human Functional Interactions (FIs) for splineTimeR package
Description:

Data set containing two complete lists of identified functional interaction partners in Human. Data are derived from Reactome and BioGRID databases.

r-flowsorted-cordbloodnorway-450k 1.38.0
Propagated dependencies: r-minfi@1.58.0
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-fourdndata 1.12.0
Propagated dependencies: r-s4vectors@0.50.1 r-iranges@2.46.0 r-hicexperiment@1.12.0 r-genomicranges@1.64.0 r-biocfilecache@3.2.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/js2264/fourDNData
Licenses: Expat
Build system: r
Synopsis: 4DN data package
Description:

fourDNData is a data package giving programmatic access to Hi-C contact matrices uniformly processed by the [4DN consortium](https://www.4dnucleome.org/). The matrices are available in the multi-resolution `.mcool` format.

r-flowmerge 2.60.0
Propagated dependencies: r-snow@0.4-4 r-rrcov@1.7-7 r-rgraphviz@2.56.0 r-graph@1.90.0 r-foreach@1.5.2 r-flowcore@2.24.0 r-flowclust@3.50.0 r-feature@1.2.16
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/flowMerge
Licenses: Artistic License 2.0
Build system: r
Synopsis: Cluster Merging for Flow Cytometry Data
Description:

Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Note: users should have a working copy of flowClust 2.0 installed.

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-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.

r-fabia 2.58.0
Propagated dependencies: r-biobase@2.72.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: http://www.bioinf.jku.at/software/fabia/fabia.html
Licenses: LGPL 2.1+
Build system: r
Synopsis: FABIA: Factor Analysis for Bicluster Acquisition
Description:

Biclustering by "Factor Analysis for Bicluster Acquisition" (FABIA). FABIA is a model-based technique for biclustering, that is clustering rows and columns simultaneously. Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns. It captures realistic non-Gaussian data distributions with heavy tails as observed in gene expression measurements. FABIA utilizes well understood model selection techniques like the EM algorithm and variational approaches and is embedded into a Bayesian framework. FABIA ranks biclusters according to their information content and separates spurious biclusters from true biclusters. The code is written in C.

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-fastranges 1.0.0
Propagated dependencies: r-s4vectors@0.50.1 r-rcpp@1.1.1-1.1 r-iranges@2.46.0 r-genomicranges@1.64.0 r-genomeinfodb@1.48.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/cparsania/fastRanges
Licenses: Artistic License 2.0
Build system: r
Synopsis: Deterministic Multithreaded Genomic Interval Operations
Description:

High-performance interval overlap and join operations for IRanges and GenomicRanges'. The package provides deterministic multithreaded overlap computation, reusable subject indexes for repeated queries, and join helpers that keep range metadata in a consistent output grammar.

r-fdb-ucsc-trnas 1.0.1
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.tRNAs
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for FeatureDb object(s)
Description:

Exposes an annotation databases generated from UCSC by exposing these as FeatureDb objects.

Page: 13233343536126
Total packages: 3017