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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-clariomsmousehttranscriptcluster-db 8.8.0
Propagated dependencies: r-org-mm-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/clariomsmousehttranscriptcluster.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix clariomsmouseht annotation data (chip clariomsmousehttranscriptcluster)
Description:

Affymetrix clariomsmouseht annotation data (chip clariomsmousehttranscriptcluster) assembled using data from public repositories.

r-cyp450cdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cyp450cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: cyp450cdf
Description:

This package provides a package containing an environment representing the CYP450.CDF file.

r-cytoglmm 1.18.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://christofseiler.github.io/CytoGLMM
Licenses: LGPL 3
Build system: r
Synopsis: Conditional Differential Analysis for Flow and Mass Cytometry Experiments
Description:

The CytoGLMM R package implements two multiple regression strategies: A bootstrapped generalized linear model (GLM) and a generalized linear mixed model (GLMM). Most current data analysis tools compare expressions across many computationally discovered cell types. CytoGLMM focuses on just one cell type. Our narrower field of application allows us to define a more specific statistical model with easier to control statistical guarantees. As a result, CytoGLMM finds differential proteins in flow and mass cytometry data while reducing biases arising from marker correlations and safeguarding against false discoveries induced by patient heterogeneity.

r-ctsge 1.36.0
Propagated dependencies: r-stringr@1.6.0 r-shiny@1.11.1 r-reshape2@1.4.5 r-limma@3.66.0 r-ggplot2@4.0.1 r-ccapp@0.3.5
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/michalsharabi/ctsGE
Licenses: GPL 2
Build system: r
Synopsis: Clustering of Time Series Gene Expression data
Description:

Methodology for supervised clustering of potentially many predictor variables, such as genes etc., in time series datasets Provides functions that help the user assigning genes to predefined set of model profiles.

r-codex 1.42.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-iranges@2.44.0 r-genomeinfodb@1.46.0 r-bsgenome-hsapiens-ucsc-hg19@1.4.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CODEX
Licenses: GPL 2
Build system: r
Synopsis: Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
Description:

This package provides a normalization and copy number variation calling procedure for whole exome DNA sequencing data. CODEX relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model in CODEX includes terms that specifically remove biases due to GC content, exon length and targeting and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data.

r-casper 2.44.0
Propagated dependencies: r-vgam@1.1-13 r-survival@3.8-3 r-sqldf@0.4-11 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rsamtools@2.26.0 r-mgcv@1.9-4 r-limma@3.66.0 r-iranges@2.44.0 r-gtools@3.9.5 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-gaga@2.56.0 r-ebarrays@2.74.0 r-coda@0.19-4.1 r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/casper
Licenses: FSDG-compatible
Build system: r
Synopsis: Characterization of Alternative Splicing based on Paired-End Reads
Description:

Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.

r-cimice 1.18.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/redsnic/CIMICE
Licenses: Artistic License 2.0
Build system: r
Synopsis: CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
Description:

CIMICE is a tool in the field of tumor phylogenetics and its goal is to build a Markov Chain (called Cancer Progression Markov Chain, CPMC) in order to model tumor subtypes evolution. The input of CIMICE is a Mutational Matrix, so a boolean matrix representing altered genes in a collection of samples. These samples are assumed to be obtained with single-cell DNA analysis techniques and the tool is specifically written to use the peculiarities of this data for the CMPC construction.

r-cmap 1.15.1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cMAP
Licenses: LGPL 2.0+
Build system: r
Synopsis: data package containing annotation data for cMAP
Description:

Annotation data file for cMAP assembled using data from public data repositories.

r-cotan 2.10.3
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/seriph78/COTAN
Licenses: GPL 3
Build system: r
Synopsis: COexpression Tables ANalysis
Description:

Statistical and computational method to analyze the co-expression of gene pairs at single cell level. It provides the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can effectively assess the correlated or anti-correlated expression of gene pairs. It provides a numerical index related to the correlation and an approximate p-value for the associated independence test. COTAN can also evaluate whether single genes are differentially expressed, scoring them with a newly defined global differentiation index. Moreover, this approach provides ways to plot and cluster genes according to their co-expression pattern with other genes, effectively helping the study of gene interactions and becoming a new tool to identify cell-identity marker genes.

r-ctdata 1.10.0
Propagated dependencies: r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CTdata
Licenses: Artistic License 2.0
Build system: r
Synopsis: Data companion to CTexploreR
Description:

Data from publicly available databases (GTEx, CCLE, TCGA and ENCODE) that go with CTexploreR in order to re-define a comprehensive and thoroughly curated list of CT genes and their main characteristics.

r-crimage 1.58.0
Propagated dependencies: r-sgeostat@1.0-27 r-mass@7.3-65 r-foreach@1.5.2 r-ebimage@4.52.0 r-e1071@1.7-16 r-dnacopy@1.84.0 r-acgh@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CRImage
Licenses: Artistic License 2.0
Build system: r
Synopsis: CRImage a package to classify cells and calculate tumour cellularity
Description:

CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.

r-clumsiddata 1.26.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CluMSIDdata
Licenses: Expat
Build system: r
Synopsis: Data for the CluMSID package
Description:

This package contains various LC-MS/MS and GC-MS data that is used in vignettes and examples in the CluMSID package.

r-crlmm 1.68.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/crlmm
Licenses: Artistic License 2.0
Build system: r
Synopsis: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
Description:

Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms.

r-cliquems 1.24.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: http://cliquems.seeslab.net
Licenses: GPL 2+
Build system: r
Synopsis: Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
Description:

Annotates data from liquid chromatography coupled to mass spectrometry (LC/MS) metabolomics experiments. Based on a network algorithm (O.Senan, A. Aguilar- Mogas, M. Navarro, O. Yanes, R.GuimerĂ  and M. Sales-Pardo, Bioinformatics, 35(20), 2019), CliqueMS builds a weighted similarity network where nodes are features and edges are weighted according to the similarity of this features. Then it searches for the most plausible division of the similarity network into cliques (fully connected components). Finally it annotates metabolites within each clique, obtaining for each annotated metabolite the neutral mass and their features, corresponding to isotopes, ionization adducts and fragmentation adducts of that metabolite.

r-cbpmanager 1.18.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://arsenij-ust.github.io/cbpManager/index.html
Licenses: FSDG-compatible
Build system: r
Synopsis: Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics
Description:

This R package provides an R Shiny application that enables the user to generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics. Create cancer studies and edit its metadata. Upload mutation data of a patient that will be concatenated to the data_mutation_extended.txt file of the study. Create and edit clinical patient data, sample data, and timeline data. Create custom timeline tracks for patients.

r-ctdquerier 2.18.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CTDquerier
Licenses: Expat
Build system: r
Synopsis: Package for CTDbase data query, visualization and downstream analysis
Description:

Package to retrieve and visualize data from the Comparative Toxicogenomics Database (http://ctdbase.org/). The downloaded data is formated as DataFrames for further downstream analyses.

r-clariomshumantranscriptcluster-db 8.8.0
Propagated dependencies: r-org-hs-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/clariomshumantranscriptcluster.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix clariomshuman annotation data (chip clariomshumantranscriptcluster)
Description:

Affymetrix clariomshuman annotation data (chip clariomshumantranscriptcluster) assembled using data from public repositories.

r-crisprbase 1.14.0
Propagated dependencies: r-stringr@1.6.0 r-s4vectors@0.48.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-biostrings@2.78.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/crisprVerse/crisprBase
Licenses: Expat
Build system: r
Synopsis: Base functions and classes for CRISPR gRNA design
Description:

This package provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates of spacer and protospacer sequences. Commonly-used CRISPR nuclease objects are provided that can be readily used in other packages. Both DNA- and RNA-targeting nucleases are supported.

r-causalr 1.42.0
Propagated dependencies: r-igraph@2.2.1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CausalR
Licenses: GPL 2+
Build system: r
Synopsis: Causal network analysis methods
Description:

Causal network analysis methods for regulator prediction and network reconstruction from genome scale data.

r-curatedbladderdata 1.46.0
Propagated dependencies: r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/lima1/curatedBladderData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Bladder Cancer Gene Expression Analysis
Description:

The curatedBladderData package provides relevant functions and data for gene expression analysis in patients with bladder cancer.

r-cnorode 1.52.0
Propagated dependencies: r-genalg@0.2.1 r-cellnoptr@1.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CNORode
Licenses: GPL 2
Build system: r
Synopsis: ODE add-on to CellNOptR
Description:

Logic based ordinary differential equation (ODE) add-on to CellNOptR.

r-cbnplot 1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/noriakis/CBNplot
Licenses: Artistic License 2.0
Build system: r
Synopsis: plot bayesian network inferred from gene expression data based on enrichment analysis results
Description:

This package provides the visualization of bayesian network inferred from gene expression data. The networks are based on enrichment analysis results inferred from packages including clusterProfiler and ReactomePA. The networks between pathways and genes inside the pathways can be inferred and visualized.

r-cosmic-67 1.46.0
Propagated dependencies: r-variantannotation@1.56.0 r-summarizedexperiment@1.40.0 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/COSMIC.67
Licenses: GPL 3
Build system: r
Synopsis: COSMIC.67
Description:

COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24).

Total results: 2911