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      /\__ \     / /\ \ \\ \ \_/ / /     / / /\ \__
     / /_ \ \   / / /\ \ \\ \___/ /     / / /\ \___\
    / / /\ \ \ / / /  \ \_\\ \ \_/      \ \ \ \/___/
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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-rgadem 2.55.0
Propagated dependencies: r-biostrings@2.78.0 r-bsgenome@1.78.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-seqlogo@1.76.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/rGADEM/
Licenses: Artistic License 2.0
Build system: r
Synopsis: De novo sequence motif discovery
Description:

rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data.

r-simpleaffy 2.66.0
Propagated dependencies: r-affy@1.88.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-gcrma@2.82.0 r-genefilter@1.92.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/simpleaffy/
Licenses: GPL 2+
Build system: r
Synopsis: Very simple high level analysis of Affymetrix data
Description:

This package provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy use of the affy library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures.

r-aims 1.42.0
Propagated dependencies: r-biobase@2.70.0 r-e1071@1.7-16
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://git.bioconductor.org/packages/AIMS
Licenses: Artistic License 2.0
Build system: r
Synopsis: Absolute assignment of breast cancer intrinsic molecular subtype
Description:

This package contains an implementation of AIMS -- Absolute Intrinsic Molecular Subtyping. It contains necessary functions to assign the five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, Normal-like). Assignments could be done on individual samples as well as on dataset of gene expression data.

r-metaneighbor 1.29.0
Propagated dependencies: r-beanplot@1.3.1 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-gplots@3.2.0 r-igraph@2.2.1 r-matrix@1.7-4 r-matrixstats@1.5.0 r-rcolorbrewer@1.1-3 r-singlecellexperiment@1.32.0 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://bioconductor.org/packages/MetaNeighbor
Licenses: Expat
Build system: r
Synopsis: Single cell replicability analysis
Description:

This package implements a method to rapidly assess cell type identity using both functional and random gene sets and it allows users to quantify cell type replicability across datasets using neighbor voting. MetaNeighbor works on the basis that cells of the same type should have more similar gene expression profiles than cells of different types.

r-conos 1.5.2
Propagated dependencies: r-abind@1.4-8 r-complexheatmap@2.26.0 r-cowplot@1.2.0 r-dendextend@1.19.1 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-gridextra@2.3 r-igraph@2.2.1 r-irlba@2.3.5.1 r-leidenalg@1.1.5 r-magrittr@2.0.4 r-matrix@1.7-4 r-n2r@1.0.3 r-r6@2.6.1 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1 r-rcppeigen@0.3.4.0.2 r-rcppprogress@0.4.2 r-reshape2@1.4.5 r-rlang@1.1.6 r-rtsne@0.17 r-sccore@1.0.6
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/kharchenkolab/conos
Licenses: GPL 3
Build system: r
Synopsis: Clustering on network of samples
Description:

This package wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. Conos focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes.

r-webbioc 1.82.0
Dependencies: netpbm@10.78.3 perl@5.36.0
Propagated dependencies: r-affy@1.88.0 r-annaffy@1.82.0 r-biobase@2.70.0 r-biocmanager@1.30.27 r-gcrma@2.82.0 r-multtest@2.66.0 r-qvalue@2.42.0 r-vsn@3.78.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/
Licenses: GPL 2+
Build system: r
Synopsis: Bioconductor web interface
Description:

This package provides an integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. Currently only Affymetrix oligonucleotide analysis is supported.

r-valr 0.8.4
Propagated dependencies: r-broom@1.0.10 r-cli@3.6.5 r-cpp11bigwig@0.1.2 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-lifecycle@1.0.4 r-rcpp@1.1.0 r-readr@2.1.6 r-rlang@1.1.6 r-stringr@1.6.0 r-tibble@3.3.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/rnabioco/valr
Licenses: Expat
Build system: r
Synopsis: Genome interval arithmetic in R
Description:

This package enables you to read and manipulate genome intervals and signals. It provides functionality similar to command-line tool suites within R, enabling interactive analysis and visualization of genome-scale data.

r-rqc 1.44.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-biocstyle@2.38.0 r-biostrings@2.78.0 r-biovizbase@1.58.0 r-genomicalignments@1.46.0 r-genomicfiles@1.46.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-knitr@1.50 r-markdown@2.0 r-plyr@1.8.9 r-rcpp@1.1.0 r-reshape2@1.4.5 r-rsamtools@2.26.0 r-s4vectors@0.48.0 r-shiny@1.11.1 r-shortread@1.68.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/labbcb/Rqc
Licenses: GPL 2+
Build system: r
Synopsis: Quality control tool for high-throughput sequencing data
Description:

Rqc is an optimized tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.

r-vsn 3.78.0
Propagated dependencies: r-affy@1.88.0 r-biobase@2.70.0 r-ggplot2@4.0.1 r-lattice@0.22-7 r-limma@3.66.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/release/bioc/html/vsn.html
Licenses: Artistic License 2.0
Build system: r
Synopsis: Variance stabilization and calibration for microarray data
Description:

The package implements a method for normalising microarray intensities, and works for single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.

r-rcas 1.36.0
Dependencies: pandoc@2.19.2
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-bsgenome@1.78.0 r-bsgenome-hsapiens-ucsc-hg19@1.4.3 r-cowplot@1.2.0 r-data-table@1.17.8 r-dt@0.34.0 r-genomation@1.42.0 r-genomeinfodb@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-gprofiler2@0.2.4 r-iranges@2.44.0 r-knitr@1.50 r-pbapply@1.7-4 r-pheatmap@1.0.13 r-plotly@4.11.0 r-plotrix@3.8-13 r-proxy@0.4-27 r-ranger@0.17.0 r-rmarkdown@2.30 r-rsqlite@2.4.4 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqlogo@1.76.0 r-txdbmaker@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/BIMSBbioinfo/RCAS
Licenses: Artistic License 2.0
Build system: r
Synopsis: RNA-centric annotation system
Description:

RCAS aims to be a standalone RNA-centric annotation system that provides intuitive reports and publication-ready graphics. This package provides the R library implementing most of the pipeline's features.

r-fgsea 1.36.0
Propagated dependencies: r-bh@1.87.0-1 r-biocparallel@1.44.0 r-cowplot@1.2.0 r-data-table@1.17.8 r-fastmatch@1.1-6 r-ggplot2@4.0.1 r-matrix@1.7-4 r-rcpp@1.1.0 r-scales@1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ctlab/fgsea/
Licenses: Expat
Build system: r
Synopsis: Fast gene set enrichment analysis
Description:

The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm makes more permutations and gets more fine grained p-values, which allows using accurate standard approaches to multiple hypothesis correction.

r-ggcyto 1.38.0
Propagated dependencies: r-data-table@1.17.8 r-flowcore@2.22.0 r-flowworkspace@4.22.0 r-ggplot2@4.0.1 r-gridextra@2.3 r-hexbin@1.28.5 r-ncdfflow@2.56.0 r-plyr@1.8.9 r-rcolorbrewer@1.1-3 r-rlang@1.1.6 r-scales@1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/RGLab/ggcyto/issues
Licenses: Artistic License 2.0
Build system: r
Synopsis: Visualize Cytometry data with ggplot
Description:

With the dedicated fortify method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. The ggcyto wrapper and some custom layers also make it easy to add gates and population statistics to the plot.

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-wiggleplotr 1.34.0
Propagated dependencies: r-assertthat@0.2.1 r-cowplot@1.2.0 r-dplyr@1.1.4 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-purrr@1.2.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/wiggleplotr/
Licenses: ASL 2.0
Build system: r
Synopsis: Make read coverage plots from BigWig files
Description:

This package provides tools to visualize read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualization of exonic read coverage.

r-dss 2.58.0
Propagated dependencies: r-biobase@2.70.0 r-biocparallel@1.44.0 r-bsseq@1.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/DSS
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: Dispersion shrinkage for sequencing data
Description:

DSS is an R library performing differential analysis for count-based sequencing data. It detects differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.

r-bsgenome-hsapiens-ucsc-hg38-masked 1.4.5
Propagated dependencies: r-bsgenome@1.78.0 r-bsgenome-hsapiens-ucsc-hg38@1.4.5 r-genomeinfodb@1.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38.masked
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full masked genomic sequences for Homo sapiens (UCSC version hg38)
Description:

This package provides the complete genome sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31). The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each of them has the 4 following masks on top:

  1. the mask of assembly gaps (AGAPS mask);

  2. the mask of intra-contig ambiguities (AMB mask);

  3. the mask of repeats from RepeatMasker (RM mask);

  4. the mask of repeats from Tandem Repeats Finder (TRF mask).

Only the AGAPS and AMB masks are "active" by default. The sequences are stored in MaskedDNAString objects.

r-biggr 1.44.0
Propagated dependencies: r-hyperdraw@1.62.0 r-hypergraph@1.82.0 r-lim@1.4.7.2 r-limsolve@2.0.1 r-rsbml@2.68.0 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BiGGR/
Licenses: GPL 3+
Build system: r
Synopsis: Constraint based modeling using metabolic reconstruction databases
Description:

This package provides an interface to simulate metabolic reconstruction from the BiGG database and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.

r-rhdf5lib 1.32.0
Propagated dependencies: hdf5@1.10.9 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Rhdf5lib
Licenses: Artistic License 2.0
Build system: r
Synopsis: HDF5 library as an R package
Description:

This package provides C and C++ HDF5 libraries for use in R packages.

r-org-bt-eg-db 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/org.Bt.eg.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Genome wide annotation for Bovine
Description:

This package provides genome wide annotations for Bovine, primarily based on mapping using Entrez Gene identifiers.

r-dropletutils 1.30.0
Propagated dependencies: r-assorthead@1.4.0 r-beachmat@2.26.0 r-bh@1.87.0-1 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-delayedarray@0.36.0 r-delayedmatrixstats@1.32.0 r-dqrng@0.4.1 r-edger@4.8.0 r-genomicranges@1.62.0 r-hdf5array@1.38.0 r-iranges@2.44.0 r-matrix@1.7-4 r-r-utils@2.13.0 r-rcpp@1.1.0 r-rhdf5@2.54.0 r-rhdf5lib@1.32.0 r-s4vectors@0.48.0 r-scuttle@1.20.0 r-singlecellexperiment@1.32.0 r-sparsearray@1.10.2 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/DropletUtils
Licenses: GPL 3
Build system: r
Synopsis: Utilities for handling single-cell droplet data
Description:

This package provides a number of utility functions for handling single-cell RNA-seq data from droplet technologies such as 10X Genomics. This includes data loading from count matrices or molecule information files, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.

r-bladderbatch 1.48.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/bladderbatch
Licenses: Artistic License 2.0
Build system: r
Synopsis: Bladder gene expression data illustrating batch effects
Description:

This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an illustrative example for the sva package.

r-org-sc-sgd-db 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/org.Sc.sgd.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Genome wide annotation for Yeast
Description:

This package provides genome wide annotation for Yeast, primarily based on mapping using ORF identifiers from SGD.

r-biocio 1.20.0
Propagated dependencies: r-biocgenerics@0.56.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BiocIO
Licenses: Artistic License 2.0
Build system: r
Synopsis: Standard input and output for Bioconductor packages
Description:

This package implements `import()` and `export()` standard generics for importing and exporting biological data formats. `import()` supports whole-file as well as chunk-wise iterative import. The `import()` interface optionally provides a standard mechanism for 'lazy' access via `filter()` (on row or element-like components of the file resource), `select()` (on column-like components of the file resource) and `collect()`. The `import()` interface optionally provides transparent access to remote (e.g. via https) as well as local access. Developers can register a file extension, e.g., `.loom` for dispatch from character-based URIs to specific `import()` / `export()` methods based on classes representing file types, e.g., `LoomFile()`.

r-hgu95av2-db 3.13.0
Propagated dependencies: r-annotationdbi@1.72.0 r-org-hs-eg-db@3.22.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/hgu95av2.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2)
Description:

This package provides Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2) assembled using data from public repositories.

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