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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-nondetects 2.40.0
Propagated dependencies: r-mvtnorm@1.3-3 r-limma@3.66.0 r-htqpcr@1.64.0 r-biobase@2.70.0 r-arm@1.14-4
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/nondetects
Licenses: GPL 3
Build system: r
Synopsis: Non-detects in qPCR data
Description:

This package provides methods to model and impute non-detects in the results of qPCR experiments.

r-netactivitydata 1.12.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/NetActivityData
Licenses: Expat
Build system: r
Synopsis: Data required for getting the gene set scores with NetActivity package
Description:

This package contains the weights from pre-trained shallow sparsely-connected autoencoders. This data is required for getting the gene set scores with NetActivity package.

r-notameviz 1.0.2
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-newwave 1.20.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-sharedobject@1.24.0 r-matrix@1.7-4 r-irlba@2.3.5.1 r-delayedarray@0.36.0 r-biocsingular@1.26.1
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/NewWave
Licenses: GPL 3
Build system: r
Synopsis: Negative binomial model for scRNA-seq
Description:

This package provides a model designed for dimensionality reduction and batch effect removal for scRNA-seq data. It is designed to be massively parallelizable using shared objects that prevent memory duplication, and it can be used with different mini-batch approaches in order to reduce time consumption. It assumes a negative binomial distribution for the data with a dispersion parameter that can be both commonwise across gene both genewise.

r-nadfinder 1.34.0
Propagated dependencies: r-trackviewer@1.46.0 r-summarizedexperiment@1.40.0 r-signal@1.8-1 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rsamtools@2.26.0 r-metap@1.12 r-limma@3.66.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicalignments@1.46.0 r-genomeinfodb@1.46.0 r-empiricalbrownsmethod@1.38.0 r-csaw@1.44.0 r-corrplot@0.95 r-biocgenerics@0.56.0 r-baseline@1.3-7 r-atacseqqc@1.34.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/NADfinder
Licenses: GPL 2+
Build system: r
Synopsis: Call wide peaks for sequencing data
Description:

Nucleolus is an important structure inside the nucleus in eukaryotic cells. It is the site for transcribing rDNA into rRNA and for assembling ribosomes, aka ribosome biogenesis. In addition, nucleoli are dynamic hubs through which numerous proteins shuttle and contact specific non-rDNA genomic loci. Deep sequencing analyses of DNA associated with isolated nucleoli (NAD- seq) have shown that specific loci, termed nucleolus- associated domains (NADs) form frequent three- dimensional associations with nucleoli. NAD-seq has been used to study the biological functions of NAD and the dynamics of NAD distribution during embryonic stem cell (ESC) differentiation. Here, we developed a Bioconductor package NADfinder for bioinformatic analysis of the NAD-seq data, including baseline correction, smoothing, normalization, peak calling, and annotation.

r-nanotube 1.16.0
Propagated dependencies: r-reshape@0.8.10 r-limma@3.66.0 r-ggplot2@4.0.1 r-fgsea@1.36.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/NanoTube
Licenses: FSDG-compatible
Build system: r
Synopsis: An Easy Pipeline for NanoString nCounter Data Analysis
Description:

NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data. Analysis functions include differential analysis and gene set analysis methods, as well as postprocessing steps to help understand the results. Additional functions are included to enable interoperability with other Bioconductor NanoString data analysis packages.

r-nxtirfdata 1.16.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://github.com/alexchwong/NxtIRFdata
Licenses: Expat
Build system: r
Synopsis: Data for NxtIRF
Description:

NxtIRFdata is a companion package for SpliceWiz, an interactive analysis and visualization tool for alternative splicing quantitation (including intron retention) for RNA-seq BAM files. NxtIRFdata contains Mappability files required for the generation of human and mouse references. NxtIRFdata also contains a synthetic genome reference and example BAM files used to demonstrate SpliceWiz's functionality. BAM files are based on 6 samples from the Leucegene dataset provided by NCBI Gene Expression Omnibus under accession number GSE67039.

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-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-nugomm1a520177cdf 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/nugomm1a520177cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: nugomm1a520177cdf
Description:

This package provides a package containing an environment representing the NuGO_Mm1a520177.cdf file.

r-ncgtw 1.24.0
Propagated dependencies: r-xcms@4.8.0 r-rcpp@1.1.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/ncGTW
Licenses: GPL 2
Build system: r
Synopsis: Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection
Description:

The purpose of ncGTW is to help XCMS for LC-MS data alignment. Currently, ncGTW can detect the misaligned feature groups by XCMS, and the user can choose to realign these feature groups by ncGTW or not.

r-notame 1.0.1
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://github.com/hanhineva-lab/notame
Licenses: Expat
Build system: r
Synopsis: Workflow for non-targeted LC-MS metabolic profiling
Description:

This package provides functionality for untargeted LC-MS metabolomics research as specified in the associated protocol article in the Metabolomics Data Processing and Data Analysis—Current Best Practices special issue of the Metabolites journal (2020). This includes tabular data preprocessing and quality control, uni- and multivariate analysis as well as quality control visualizations, feature-wise visualizations and results visualizations. Raw data preprocessing and functionality related to biological context, such as pathway analysis, is not included.

r-netpathminer 1.46.0
Dependencies: libxml2@2.14.6 libsbml@5.20.5
Propagated dependencies: r-igraph@2.2.1
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://github.com/ahmohamed/NetPathMiner
Licenses: GPL 2+
Build system: r
Synopsis: NetPathMiner for Biological Network Construction, Path Mining and Visualization
Description:

NetPathMiner is a general framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations, metabolic, reaction and gene representations. NetPathMiner finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation.

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-nullranges 1.16.3
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-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-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-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-netboost 2.18.1
Dependencies: perl@5.36.0 gzip@1.14 bash@5.2.37
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/release/bioc/html/netboost.html
Licenses: GPL 3
Build system: r
Synopsis: Network Analysis Supported by Boosting
Description:

Boosting supported network analysis for high-dimensional omics applications.

r-nparc 1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/NPARC
Licenses: GPL 3
Build system: r
Synopsis: Non-parametric analysis of response curves for thermal proteome profiling experiments
Description:

Perform non-parametric analysis of response curves as described by Childs, Bach, Franken et al. (2019): Non-parametric analysis of thermal proteome profiles reveals novel drug-binding proteins.

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-npgsea 1.46.0
Propagated dependencies: r-gseabase@1.72.0 r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/npGSEA
Licenses: Artistic License 2.0
Build system: r
Synopsis: Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)
Description:

Current gene set enrichment methods rely upon permutations for inference. These approaches are computationally expensive and have minimum achievable p-values based on the number of permutations, not on the actual observed statistics. We have derived three parametric approximations to the permutation distributions of two gene set enrichment test statistics. We are able to reduce the computational burden and granularity issues of permutation testing with our method, which is implemented in this package. npGSEA calculates gene set enrichment statistics and p-values without the computational cost of permutations. It is applicable in settings where one or many gene sets are of interest. There are also built-in plotting functions to help users visualize results.

r-nugohs1a520180probe 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/nugohs1a520180probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type nugohs1a520180
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-nmrdata 1.0.0
Propagated dependencies: r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://github.com/tkimhofer/nmrdata
Licenses: Expat
Build system: r
Synopsis: Example 1d NMR Data for Metabolic Profiling
Description:

This package provides example one-dimensional proton NMR spectra of murine urine samples collected before and after bariatric or sham surgery (Roux-en-Y gastric bypass). The data are adapted from Jia V Li et al. (2011), "Metabolic surgery profoundly influences gut microbial-host metabolic cross-talk", Gut, 60(9), 1214–1223. <doi:10.1136/gut.2010.234708>. This package serves as example data for metabolomics analysis and teaching purposes.

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Total results: 69112