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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-nanotubes 1.26.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://github.com/MalteThodberg/nanotubes
Licenses: GPL 3
Build system: r
Synopsis: Mouse nanotube CAGE data
Description:

Cap Analysis of Gene Expression (CAGE) data from "Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo" by Bornholdt et al. supplied as CAGE Transcription Start Sites (CTSSs).

r-ntw 1.60.0
Propagated dependencies: r-mvtnorm@1.3-3
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/NTW
Licenses: GPL 2
Build system: r
Synopsis: Predict gene network using an Ordinary Differential Equation (ODE) based method
Description:

This package predicts the gene-gene interaction network and identifies the direct transcriptional targets of the perturbation using an ODE (Ordinary Differential Equation) based method.

r-nupop 2.18.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/NuPoP
Licenses: GPL 2
Build system: r
Synopsis: An R package for nucleosome positioning prediction
Description:

NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at https://github.com/jipingw. The Fortran codes have complete functonality as the R package. Note: NuPoP has two separate functions for prediction of nucleosome positioning, one for MNase-map trained models and the other for chemical map-trained models. The latter was implemented for four species including yeast, S.pombe, mouse and human, trained based on our recent publications. We noticed there is another package nuCpos by another group for prediction of nucleosome positioning trained with chemicals. A report to compare recent versions of NuPoP with nuCpos can be found at https://github.com/jiping/NuPoP_doc. Some more information can be found and will be posted at https://github.com/jipingw/NuPoP.

r-netresponse 1.70.0
Propagated dependencies: r-rmarkdown@2.30 r-rgraphviz@2.54.0 r-reshape2@1.4.5 r-rcolorbrewer@1.1-3 r-qvalue@2.42.0 r-plyr@1.8.9 r-minet@3.68.0 r-mclust@6.1.2 r-igraph@2.2.1 r-graph@1.88.0 r-ggplot2@4.0.1 r-biocstyle@2.38.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://github.com/antagomir/netresponse
Licenses: FSDG-compatible
Build system: r
Synopsis: Functional Network Analysis
Description:

Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling.

r-notamestats 1.0.0
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-notame@1.0.1 r-dplyr@1.1.4 r-broom@1.0.10 r-biocparallel@1.44.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://github.com/hanhineva-lab/notameStats
Licenses: Expat
Build system: r
Synopsis: Workflow for non-targeted LC-MS metabolic profiling
Description:

This package provides univariate and multivariate statistics for feature prioritization in untargeted LC-MS metabolomics research.

r-ndexr 1.32.0
Propagated dependencies: r-tidyr@1.3.1 r-rcx@1.14.1 r-plyr@1.8.9 r-jsonlite@2.0.0 r-httr@1.4.7
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://github.com/frankkramer-lab/ndexr
Licenses: Modified BSD
Build system: r
Synopsis: NDEx R client library
Description:

This package offers an interface to NDEx servers, e.g. the public server at http://ndexbio.org/. It can retrieve and save networks via the API. Networks are offered as RCX object and as igraph representation.

r-normalyzerde 1.28.0
Propagated dependencies: r-vsn@3.78.0 r-summarizedexperiment@1.40.0 r-preprocesscore@1.72.0 r-matrixstats@1.5.0 r-mass@7.3-65 r-limma@3.66.0 r-ggplot2@4.0.1 r-ggforce@0.5.0 r-car@3.1-3 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://github.com/ComputationalProteomics/NormalyzerDE
Licenses: Artistic License 2.0
Build system: r
Synopsis: Evaluation of normalization methods and calculation of differential expression analysis statistics
Description:

NormalyzerDE provides screening of normalization methods for LC-MS based expression data. It calculates a range of normalized matrices using both existing approaches and a novel time-segmented approach, calculates performance measures and generates an evaluation report. Furthermore, it provides an easy utility for Limma- or ANOVA- based differential expression analysis.

r-netprior 1.36.0
Propagated dependencies: r-sparsemvn@0.2.2 r-proc@1.19.0.1 r-matrix@1.7-4 r-gridextra@2.3 r-ggplot2@4.0.1 r-foreach@1.5.2 r-dplyr@1.1.4 r-doparallel@1.0.17
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: http://bioconductor.org/packages/netprioR
Licenses: GPL 3
Build system: r
Synopsis: model for network-based prioritisation of genes
Description:

This package provides a model for semi-supervised prioritisation of genes integrating network data, phenotypes and additional prior knowledge about TP and TN gene labels from the literature or experts.

r-ncigraphdata 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/NCIgraphData
Licenses: GPL 3
Build system: r
Synopsis: Data for the NCIgraph software package
Description:

This package provides pathways from the NCI Pathways Database as R graph objects.

r-netsmooth 1.30.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-scater@1.38.0 r-matrix@1.7-4 r-hdf5array@1.38.0 r-entropy@1.3.2 r-delayedarray@0.36.0 r-data-table@1.17.8 r-clusterexperiment@2.30.0 r-cluster@2.1.8.1
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://github.com/BIMSBbioinfo/netSmooth
Licenses: GPL 3
Build system: r
Synopsis: Network smoothing for scRNAseq
Description:

netSmooth is an R package for network smoothing of single cell RNA sequencing data. Using bio networks such as protein-protein interactions as priors for gene co-expression, netsmooth improves cell type identification from noisy, sparse scRNAseq data.

r-nucleosim 1.38.0
Propagated dependencies: r-s4vectors@0.48.0 r-iranges@2.44.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://github.com/arnauddroitlab/nucleoSim
Licenses: Artistic License 2.0
Build system: r
Synopsis: Generate synthetic nucleosome maps
Description:

This package can generate a synthetic map with reads covering the nucleosome regions as well as a synthetic map with forward and reverse reads emulating next-generation sequencing. The synthetic hybridization data of “Tiling Arrays” can also be generated. The user has choice between three different distributions for the read positioning: Normal, Student and Uniform. In addition, a visualization tool is provided to explore the synthetic nucleosome maps.

r-nnsvg 1.14.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-spatialexperiment@1.20.0 r-singlecellexperiment@1.32.0 r-matrixstats@1.5.0 r-matrix@1.7-4 r-brisc@1.0.6 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://github.com/lmweber/nnSVG
Licenses: Expat
Build system: r
Synopsis: Scalable identification of spatially variable genes in spatially-resolved transcriptomics data
Description:

Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more spatial locations.

r-notameviz 1.0.2
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-scales@1.4.0 r-notame@1.0.1 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-ggdendro@0.2.0 r-ggbeeswarm@0.7.2 r-dplyr@1.1.4 r-devemf@4.5-1 r-cowplot@1.2.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://github.com/hanhineva-lab/notameViz
Licenses: Expat
Build system: r
Synopsis: Workflow for non-targeted LC-MS metabolic profiling
Description:

This package provides visualization functionality for untargeted LC-MS metabolomics research. Includes quality control visualizations, feature-wise visualizations and results visualizations.

r-nullranges 1.16.3
Propagated dependencies: r-seqinfo@1.0.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-rlang@1.1.6 r-progress@1.2.3 r-plyranges@1.30.1 r-iranges@2.44.0 r-interactionset@1.38.0 r-ggridges@0.5.7 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://nullranges.github.io/nullranges
Licenses: GPL 3
Build system: r
Synopsis: Generation of null ranges via bootstrapping or covariate matching
Description:

Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrap samples of ranges (using the block bootstrap framework of Bickel et al 2010), or sets of control ranges that are matched across one or more covariates. nullranges is designed to be inter-operable with other packages for analysis of genomic overlap enrichment, including the plyranges Bioconductor package.

r-nempi 1.18.0
Propagated dependencies: r-randomforest@4.7-1.2 r-nnet@7.3-20 r-naturalsort@0.1.3 r-mnem@1.26.0 r-matrixstats@1.5.0 r-epinem@1.34.0 r-e1071@1.7-16
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://github.com/cbg-ethz/nempi/
Licenses: GPL 3
Build system: r
Synopsis: Inferring unobserved perturbations from gene expression data
Description:

Takes as input an incomplete perturbation profile and differential gene expression in log odds and infers unobserved perturbations and augments observed ones. The inference is done by iteratively inferring a network from the perturbations and inferring perturbations from the network. The network inference is done by Nested Effects Models.

r-nugomm1a520177probe 3.4.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/nugomm1a520177probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type nugomm1a520177
Description:

This package was automatically created by package AnnotationForge version 1.11.20. The probe sequence data was obtained from http://www.affymetrix.com.

r-nugohs1a520180-db 3.4.0
Propagated dependencies: r-org-hs-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/nugohs1a520180.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix nugohs1a520180 annotation data (chip nugohs1a520180)
Description:

Affymetrix nugohs1a520180 annotation data (chip nugohs1a520180) assembled using data from public repositories.

r-nugohs1a520180cdf 3.4.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/nugohs1a520180cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: nugohs1a520180cdf
Description:

This package provides a package containing an environment representing the NuGO_Hs1a520180.cdf file.

r-normr 1.36.0
Propagated dependencies: r-rtracklayer@1.70.0 r-rcpp@1.1.0 r-qvalue@2.42.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-bamsignals@1.42.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://github.com/your-highness/normR
Licenses: GPL 2
Build system: r
Synopsis: Normalization and difference calling in ChIP-seq data
Description:

Robust normalization and difference calling procedures for ChIP-seq and alike data. Read counts are modeled jointly as a binomial mixture model with a user-specified number of components. A fitted background estimate accounts for the effect of enrichment in certain regions and, therefore, represents an appropriate null hypothesis. This robust background is used to identify significantly enriched or depleted regions.

r-nucpos 1.28.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/nuCpos
Licenses: GPL 2
Build system: r
Synopsis: An R package for prediction of nucleosome positions
Description:

nuCpos, a derivative of NuPoP, is an R package for prediction of nucleosome positions. nuCpos calculates local and whole nucleosomal histone binding affinity (HBA) scores for a given 147-bp sequence. Note: This package was designed to demonstrate the use of chemical maps in prediction. As the parental package NuPoP now provides chemical-map-based prediction, the function for dHMM-based prediction was removed from this package. nuCpos continues to provide functions for HBA calculation.

r-ncrnatools 1.20.0
Propagated dependencies: r-xml2@1.5.0 r-s4vectors@0.48.0 r-iranges@2.44.0 r-httr@1.4.7 r-ggplot2@4.0.1 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/ncRNAtools
Licenses: GPL 3
Build system: r
Synopsis: An R toolkit for non-coding RNA
Description:

ncRNAtools provides a set of basic tools for handling and analyzing non-coding RNAs. These include tools to access the RNAcentral database and to predict and visualize the secondary structure of non-coding RNAs. The package also provides tools to read, write and interconvert the file formats most commonly used for representing such secondary structures.

r-onlinefdr 2.18.0
Propagated dependencies: r-rcppprogress@0.4.2 r-rcpp@1.1.0 r-progress@1.2.3
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://dsrobertson.github.io/onlineFDR/index.html
Licenses: GPL 3
Build system: r
Synopsis: Online error rate control
Description:

This package allows users to control the false discovery rate (FDR) or familywise error rate (FWER) for online multiple hypothesis testing, where hypotheses arrive in a stream. In this framework, a null hypothesis is rejected based on the evidence against it and on the previous rejection decisions.

r-omicsgmf 1.0.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-sgdgmf@1.0.1 r-scuttle@1.20.0 r-scater@1.38.0 r-s4vectors@0.48.0 r-qfeatures@1.20.0 r-matrixgenerics@1.22.0 r-matrix@1.7-4 r-ggplot2@4.0.1 r-delayedarray@0.36.0 r-biocsingular@1.26.1 r-biocparallel@1.44.0 r-beachmat@2.26.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://github.com/statOmics/omicsGMF
Licenses: Artistic License 2.0
Build system: r
Synopsis: Dimensionality reduction of (single-cell) omics data in R using omicsGMF
Description:

omicsGMF is a Bioconductor package that uses the sgdGMF-framework of the \codesgdGMF package for highly performant and fast matrix factorization that can be used for dimensionality reduction, visualization and imputation of omics data. It considers data from the general exponential family as input, and therefore suits the use of both RNA-seq (Poisson or Negative Binomial data) and proteomics data (Gaussian data). It does not require prior transformation of counts to the log-scale, because it rather optimizes the deviances from the data family specified. Also, it allows to correct for known sample-level and feature-level covariates, therefore enabling visualization and dimensionality reduction upon batch correction. Last but not least, it deals with missing values, and allows to impute these after matrix factorization, useful for proteomics data. This Bioconductor package allows input of SummarizedExperiment, SingleCellExperiment, and QFeature classes.

r-ocplus 1.84.0
Propagated dependencies: r-multtest@2.66.0 r-interp@1.1-6
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/OCplus
Licenses: LGPL 2.0+
Build system: r
Synopsis: Operating characteristics plus sample size and local fdr for microarray experiments
Description:

This package allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes).

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Total results: 68655