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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-cfdnakit 1.8.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cfdnakit
Licenses: GPL 3
Build system: r
Synopsis: Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)
Description:

This package provides basic functions for analyzing shallow whole-genome sequencing (~0.3X or more) of cell-free DNA (cfDNA). The package basically extracts the length of cfDNA fragments and aids the vistualization of fragment-length information. The package also extract fragment-length information per non-overlapping fixed-sized bins and used it for calculating ctDNA estimation score (CES).

r-cetf 1.22.0
Dependencies: zlib@1.3.1 zlib@1.3.1 libxml2@2.14.6 openssl@3.0.8 gfortran@14.3.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CeTF
Licenses: GPL 3
Build system: r
Synopsis: Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Description:

This package provides the necessary functions for performing the Partial Correlation coefficient with Information Theory (PCIT) (Reverter and Chan 2008) and Regulatory Impact Factors (RIF) (Reverter et al. 2010) algorithm. The PCIT algorithm identifies meaningful correlations to define edges in a weighted network and can be applied to any correlation-based network including but not limited to gene co-expression networks, while the RIF algorithm identify critical Transcription Factors (TF) from gene expression data. These two algorithms when combined provide a very relevant layer of information for gene expression studies (Microarray, RNA-seq and single-cell RNA-seq data).

r-cycle 1.64.0
Propagated dependencies: r-mfuzz@2.70.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: http://cycle.sysbiolab.eu
Licenses: GPL 2
Build system: r
Synopsis: Significance of periodic expression pattern in time-series data
Description:

Package for assessing the statistical significance of periodic expression based on Fourier analysis and comparison with data generated by different background models.

r-cytomethic 1.6.0
Propagated dependencies: r-sesamedata@1.28.0 r-sesame@1.28.0 r-experimenthub@3.0.0 r-biocparallel@1.44.0 r-biocmanager@1.30.27
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/zhou-lab/CytoMethIC
Licenses: Artistic License 2.0
Build system: r
Synopsis: DNA methylation-based machine learning models
Description:

This package provides model data and functions for easily using machine learning models that use data from the DNA methylome to classify cancer type and phenotype from a sample. The primary motivation for the development of this package is to abstract away the granular and accessibility-limiting code required to utilize machine learning models in R. Our package provides this abstraction for RandomForest, e1071 Support Vector, Extreme Gradient Boosting, and Tensorflow models. This is paired with an ExperimentHub component, which contains models developed for epigenetic cancer classification and predicting phenotypes. This includes CNS tumor classification, Pan-cancer classification, race prediction, cell of origin classification, and subtype classification models. The package links to our models on ExperimentHub. The package currently supports HM450, EPIC, EPICv2, MSA, and MM285.

r-caen 1.18.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-poiclaclu@1.0.2.1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CAEN
Licenses: GPL 2
Build system: r
Synopsis: Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
Description:

With the development of high-throughput techniques, more and more gene expression analysis tend to replace hybridization-based microarrays with the revolutionary technology.The novel method encodes the category again by employing the rank of samples for each gene in each class. We then consider the correlation coefficient of gene and class with rank of sample and new rank of category. The highest correlation coefficient genes are considered as the feature genes which are most effective to classify the samples.

r-cnordt 1.52.0
Propagated dependencies: r-cellnoptr@1.56.0 r-abind@1.4-8
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CNORdt
Licenses: GPL 2
Build system: r
Synopsis: Add-on to CellNOptR: Discretized time treatments
Description:

This add-on to the package CellNOptR handles time-course data, as opposed to steady state data in CellNOptR. It scales the simulation step to allow comparison and model fitting for time-course data. Future versions will optimize delays and strengths for each edge.

r-citefuse 1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CiteFuse
Licenses: GPL 3
Build system: r
Synopsis: CiteFuse: multi-modal analysis of CITE-seq data
Description:

CiteFuse pacakage implements a suite of methods and tools for CITE-seq data from pre-processing to integrative analytics, including doublet detection, network-based modality integration, cell type clustering, differential RNA and protein expression analysis, ADT evaluation, ligand-receptor interaction analysis, and interactive web-based visualisation of the analyses.

r-centreprecomputed 1.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/slrvv/CENTREprecomputed
Licenses: Artistic License 2.0
Build system: r
Synopsis: Hub package for the precomputed data of CENTRE and example data
Description:

Interface and documentation for the Experiment Hub records needed by the CENTRE Bioconductor software package. The Experiment Hub records contains the precomputed fisher combined p-values, CRUP correlations. Additionally, the records hold ChIP-seq and RNA-seq data used for the example of the software package.

r-compran 1.18.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/ComPrAn
Licenses: Expat
Build system: r
Synopsis: Complexome Profiling Analysis package
Description:

This package is for analysis of SILAC labeled complexome profiling data. It uses peptide table in tab-delimited format as an input and produces ready-to-use tables and plots.

r-chimeraviz 1.36.0
Dependencies: samtools@1.19 bowtie@2.3.4.3
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/stianlagstad/chimeraviz
Licenses: Artistic License 2.0
Build system: r
Synopsis: Visualization tools for gene fusions
Description:

chimeraviz manages data from fusion gene finders and provides useful visualization tools.

r-cpvsnp 1.42.0
Propagated dependencies: r-plyr@1.8.9 r-gseabase@1.72.0 r-ggplot2@4.0.1 r-genomicfeatures@1.62.0 r-corpcor@1.6.10 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cpvSNP
Licenses: Artistic License 2.0
Build system: r
Synopsis: Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Description:

Gene set analysis methods exist to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. This package implements two such methods that require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs. Built-in plotting functions are available to help users visualize results.

r-clusterjudge 1.32.0
Propagated dependencies: r-latticeextra@0.6-31 r-lattice@0.22-7 r-jsonlite@2.0.0 r-infotheo@1.2.0.1 r-httr@1.4.7
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/ClusterJudge
Licenses: Artistic License 2.0
Build system: r
Synopsis: Judging Quality of Clustering Methods using Mutual Information
Description:

ClusterJudge implements the functions, examples and other software published as an algorithm by Gibbons, FD and Roth FP. The article is called "Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation" and it appeared in Genome Research, vol. 12, pp1574-1581 (2002). See package?ClusterJudge for an overview.

r-chipanalyser 1.32.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/ChIPanalyser
Licenses: GPL 3
Build system: r
Synopsis: ChIPanalyser: Predicting Transcription Factor Binding Sites
Description:

ChIPanalyser is a package to predict and understand TF binding by utilizing a statistical thermodynamic model. The model incorporates 4 main factors thought to drive TF binding: Chromatin State, Binding energy, Number of bound molecules and a scaling factor modulating TF binding affinity. Taken together, ChIPanalyser produces ChIP-like profiles that closely mimic the patterns seens in real ChIP-seq data.

r-celegansprobe 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/celegansprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type celegans
Description:

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was C\_elegans\_probe\_tab.

r-cmap2data 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cMap2data
Licenses: GPL 3
Build system: r
Synopsis: Connectivity Map (version 2) Data
Description:

Data package which provides default drug profiles for the DrugVsDisease package as well as associated gene lists and data clusters used by the DrugVsDisease package.

r-clustifyrdatahub 1.20.0
Propagated dependencies: r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://rnabioco.github.io/clustifyrdatahub/
Licenses: Expat
Build system: r
Synopsis: External data sets for clustifyr in ExperimentHub
Description:

References made from external single-cell mRNA sequencing data sets, stored as average gene expression matrices. For use with clustifyr <https://bioconductor.org/packages/clustifyr> to assign cell type identities.

r-compepitools 1.44.0
Propagated dependencies: r-xvector@0.50.0 r-topgo@2.62.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-methylpipe@1.44.0 r-iranges@2.44.0 r-gplots@3.2.0 r-go-db@3.22.0 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-biostrings@2.78.0 r-biocgenerics@0.56.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/compEpiTools
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: Tools for computational epigenomics
Description:

This package provides tools for computational epigenomics developed for the analysis, integration and simultaneous visualization of various (epi)genomics data types across multiple genomic regions in multiple samples.

r-connectivitymap 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/ConnectivityMap
Licenses: GPL 3
Build system: r
Synopsis: Functional connections between drugs, genes and diseases as revealed by common gene-expression changes
Description:

The Broad Institute's Connectivity Map (cmap02) is a "large reference catalogue of gene-expression data from cultured human cells perturbed with many chemicals and genetic reagents", containing more than 7000 gene expression profiles and 1300 small molecules.

r-cssq 1.22.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rsamtools@2.26.0 r-iranges@2.44.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomicalignments@1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CSSQ
Licenses: Artistic License 2.0
Build system: r
Synopsis: Chip-seq Signal Quantifier Pipeline
Description:

This package is desgined to perform statistical analysis to identify statistically significant differentially bound regions between multiple groups of ChIP-seq dataset.

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-copynumberplots 1.26.0
Propagated dependencies: r-variantannotation@1.56.0 r-summarizedexperiment@1.40.0 r-rsamtools@2.26.0 r-rhdf5@2.54.0 r-regioner@1.42.0 r-karyoploter@1.36.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-cn-mops@1.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/bernatgel/CopyNumberPlots
Licenses: Artistic License 2.0
Build system: r
Synopsis: Create Copy-Number Plots using karyoploteR functionality
Description:

CopyNumberPlots have a set of functions extending karyoploteRs functionality to create beautiful, customizable and flexible plots of copy-number related data.

r-curatedadipoarray 1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/MahShaaban/curatedAdipoArray
Licenses: FSDG-compatible
Build system: r
Synopsis: Curated Microarrays Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Under Genetic and Pharmacological Perturbations
Description:

This package provides a curated dataset of Microarrays samples. The samples are MDI- induced pre-adipocytes (3T3-L1) at different time points/stage of differentiation under different types of genetic (knockdown/overexpression) and pharmacological (drug treatment) perturbations. The package documents the data collection and processing. In addition to the documentation, the package contains the scripts that was used to generated the data.

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-coveb 1.36.0
Propagated dependencies: r-mvtnorm@1.3-3 r-matrix@1.7-4 r-laplacesdemon@16.1.6 r-igraph@2.2.1 r-gsl@2.1-9 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/covEB
Licenses: GPL 3
Build system: r
Synopsis: Empirical Bayes estimate of block diagonal covariance matrices
Description:

Using bayesian methods to estimate correlation matrices assuming that they can be written and estimated as block diagonal matrices. These block diagonal matrices are determined using shrinkage parameters that values below this parameter to zero.

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Total results: 69112