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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-lbe 1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/LBE
Licenses: GPL 2
Build system: r
Synopsis: Estimation of the false discovery rate
Description:

LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis.

r-lola 1.40.1
Propagated dependencies: r-s4vectors@0.48.0 r-reshape2@1.4.5 r-iranges@2.44.0 r-genomicranges@1.62.0 r-data-table@1.17.8 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: http://code.databio.org/LOLA
Licenses: GPL 3
Build system: r
Synopsis: Locus overlap analysis for enrichment of genomic ranges
Description:

This package provides functions for testing overlap of sets of genomic regions with public and custom region set (genomic ranges) databases. This makes it possible to do automated enrichment analysis for genomic region sets, thus facilitating interpretation of functional genomics and epigenomics data.

r-lheuristic 1.2.0
Propagated dependencies: r-multiassayexperiment@1.36.1 r-hmisc@5.2-4 r-ggpubr@0.6.2 r-ggplot2@4.0.1 r-energy@1.7-12
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://github.com/ASPresearch/Lheuristic
Licenses: Expat
Build system: r
Synopsis: Detection of scatterplots with L-shaped pattern
Description:

The Lheuristic package identifies scatterpots that follow and L-shaped, negative distribution. It can be used to identify genes regulated by methylation by integration of an expression and a methylation array. The package uses two different methods to detect expression and methyaltion L- shapped scatterplots. The parameters can be changed to detect other scatterplot patterns.

r-leebamviews 1.46.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicalignments@1.46.0 r-bsgenome@1.78.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/leeBamViews
Licenses: FSDG-compatible
Build system: r
Synopsis: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009
Description:

data from PMID 19096707; prototype for managing multiple NGS samples.

r-mogene10stv1probe 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mogene10stv1probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type mogene10stv1
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 MoGene-1\_0-st-v1\_probe\_tab.

r-mspurity 1.36.0
Propagated dependencies: r-stringr@1.6.0 r-rsqlite@2.4.4 r-reshape2@1.4.5 r-rcpp@1.1.0 r-plyr@1.8.9 r-mzr@2.44.0 r-magrittr@2.0.4 r-ggplot2@4.0.1 r-foreach@1.5.2 r-fastcluster@1.3.0 r-dplyr@1.1.4 r-dosnow@1.0.20 r-dbplyr@2.5.1 r-dbi@1.2.3
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/computational-metabolomics/msPurity/
Licenses: FSDG-compatible
Build system: r
Synopsis: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Description:

msPurity R package was developed to: 1) Assess the spectral quality of fragmentation spectra by evaluating the "precursor ion purity". 2) Process fragmentation spectra. 3) Perform spectral matching. What is precursor ion purity? -What we call "Precursor ion purity" is a measure of the contribution of a selected precursor peak in an isolation window used for fragmentation. The simple calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window. When assessing MS/MS spectra this calculation is done before and after the MS/MS scan of interest and the purity is interpolated at the recorded time of the MS/MS acquisition. Additionally, isotopic peaks can be removed, low abundance peaks are removed that are thought to have limited contribution to the resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used to normalise the intensities used for the calculation.

r-macorrplot 1.80.0
Propagated dependencies: r-lattice@0.22-7
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15799785
Licenses: GPL 2+
Build system: r
Synopsis: Visualize artificial correlation in microarray data
Description:

Graphically displays correlation in microarray data that is due to insufficient normalization.

r-m6aboost 1.16.0
Propagated dependencies: r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-experimenthub@3.0.0 r-dplyr@1.1.4 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-adabag@5.1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/ZarnackGroup/m6Aboost
Licenses: Artistic License 2.0
Build system: r
Synopsis: m6Aboost
Description:

This package can help user to run the m6Aboost model on their own miCLIP2 data. The package includes functions to assign the read counts and get the features to run the m6Aboost model. The miCLIP2 data should be stored in a GRanges object. More details can be found in the vignette.

r-msstatslobd 1.18.0
Propagated dependencies: r-rcpp@1.1.0 r-minpack-lm@1.2-4 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MSstatsLOBD
Licenses: Artistic License 2.0
Build system: r
Synopsis: Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)
Description:

The MSstatsLOBD package allows calculation and visualization of limit of blac (LOB) and limit of detection (LOD). We define the LOB as the highest apparent concentration of a peptide expected when replicates of a blank sample containing no peptides are measured. The LOD is defined as the measured concentration value for which the probability of falsely claiming the absence of a peptide in the sample is 0.05, given a probability 0.05 of falsely claiming its presence. These functionalities were previously a part of the MSstats package. The methodology is described in Galitzine (2018) <doi:10.1074/mcp.RA117.000322>.

r-mulcom 1.60.0
Propagated dependencies: r-fields@17.1 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/Mulcom
Licenses: GPL 2
Build system: r
Synopsis: Calculates Mulcom test
Description:

Identification of differentially expressed genes and false discovery rate (FDR) calculation by Multiple Comparison test.

r-mgu74ccdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mgu74ccdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: mgu74ccdf
Description:

This package provides a package containing an environment representing the MG_U74C.cdf file.

r-mu6500subdcdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mu6500subdcdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: mu6500subdcdf
Description:

This package provides a package containing an environment representing the Mu6500subD.CDF file.

r-methylseqdata 1.20.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-rhdf5@2.54.0 r-iranges@2.44.0 r-hdf5array@1.38.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MethylSeqData
Licenses: CC0
Build system: r
Synopsis: Collection of Public DNA Methylation Sequencing Datasets
Description:

Base-level (i.e. cytosine-level) counts for a collection of public bisulfite-seq datasets (e.g., WGBS and RRBS), provided as SummarizedExperiment objects with sample- and base-level metadata.

r-meebodata 1.48.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MEEBOdata
Licenses: LGPL 2.0+
Build system: r
Synopsis: MEEBO set and MEEBO controls
Description:

R objects describing the MEEBO set.

r-marker 1.0.0
Propagated dependencies: r-tibble@3.3.0 r-scales@1.4.0 r-rstatix@0.7.3 r-reshape2@1.4.5 r-rcolorbrewer@1.1-3 r-proc@1.19.0.1 r-msigdbr@25.1.1 r-limma@3.66.0 r-gridextra@2.3 r-ggrepel@0.9.6 r-ggpubr@0.6.2 r-ggplot2@4.0.1 r-ggh4x@0.3.1 r-fgsea@1.36.0 r-effectsize@1.0.1 r-edger@4.8.0 r-complexheatmap@2.26.0 r-circlize@0.4.16
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://diseasetranscriptomicslab.github.io/markeR/
Licenses: Artistic License 2.0
Build system: r
Synopsis: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers
Description:

markeR is an R package that provides a modular and extensible framework for the systematic evaluation of gene sets as phenotypic markers using transcriptomic data. The package is designed to support both quantitative analyses and visual exploration of gene set behaviour across experimental and clinical phenotypes. It implements multiple methods, including score-based and enrichment approaches, and also allows the exploration of expression behaviour of individual genes. In addition, users can assess the similarity of their own gene sets against established collections (e.g., those from MSigDB), facilitating biological interpretation.

r-micrornaome 1.32.0
Propagated dependencies: r-summarizedexperiment@1.40.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/microRNAome
Licenses: GPL 2+
Build system: r
Synopsis: SummarizedExperiment for the microRNAome project
Description:

This package provides a SummarizedExperiment object of read counts for microRNAs across tissues, cell-types, and cancer cell-lines. The read count matrix was prepared and provided by the author of the study: Towards the human cellular microRNAome.

r-macsdata 1.18.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MACSdata
Licenses: FSDG-compatible
Build system: r
Synopsis: Test datasets for the MACSr package
Description:

Test datasets from the MACS3 test examples are use in the examples of the `MACSr` package. All 9 datasets are uploaded to the `ExperimentHub`. The original data can be found at: https://github.com/macs3-project/MACS/.

r-maskbad 1.54.0
Propagated dependencies: r-gcrma@2.82.0 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/maskBAD
Licenses: GPL 2+
Build system: r
Synopsis: Masking probes with binding affinity differences
Description:

Package includes functions to analyze and mask microarray expression data.

r-mslp 1.12.0
Propagated dependencies: r-rankprod@3.36.0 r-randomforest@4.7-1.2 r-proc@1.19.0.1 r-org-hs-eg-db@3.22.0 r-magrittr@2.0.4 r-foreach@1.5.2 r-fmsb@0.7.6 r-dorng@1.8.6.2 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mslp
Licenses: GPL 3
Build system: r
Synopsis: Predict synthetic lethal partners of tumour mutations
Description:

An integrated pipeline to predict the potential synthetic lethality partners (SLPs) of tumour mutations, based on gene expression, mutation profiling and cell line genetic screens data. It has builtd-in support for data from cBioPortal. The primary SLPs correlating with muations in WT and compensating for the loss of function of mutations are predicted by random forest based methods (GENIE3) and Rank Products, respectively. Genetic screens are employed to identfy consensus SLPs leads to reduced cell viability when perturbed.

r-metamsdata 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/metaMSdata
Licenses: GPL 2+
Build system: r
Synopsis: Example CDF data for the metaMS package
Description:

Example CDF data for the metaMS package.

r-metabcombiner 1.20.0
Propagated dependencies: r-tidyr@1.3.1 r-s4vectors@0.48.0 r-rlang@1.1.6 r-mgcv@1.9-4 r-matrixstats@1.5.0 r-dplyr@1.1.4 r-caret@7.0-1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/metabCombiner
Licenses: GPL 3
Build system: r
Synopsis: Method for Combining LC-MS Metabolomics Feature Measurements
Description:

This package aligns LC-HRMS metabolomics datasets acquired from biologically similar specimens analyzed under similar, but not necessarily identical, conditions. Peak-picked and simply aligned metabolomics feature tables (consisting of m/z, rt, and per-sample abundance measurements, plus optional identifiers & adduct annotations) are accepted as input. The package outputs a combined table of feature pair alignments, organized into groups of similar m/z, and ranked by a similarity score. Input tables are assumed to be acquired using similar (but not necessarily identical) analytical methods.

r-methped 1.38.0
Propagated dependencies: r-randomforest@4.7-1.2 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MethPed
Licenses: GPL 2
Build system: r
Synopsis: DNA methylation classifier tool for the identification of pediatric brain tumor subtypes
Description:

Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. For this aim, we developed a diagnostic classifier based on DNA methylation profiles. We offer MethPed as an easy-to-use toolbox that allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors. The current version of MethPed can classify the following tumor diagnoses/subgroups: Diffuse Intrinsic Pontine Glioma (DIPG), Ependymoma, Embryonal tumors with multilayered rosettes (ETMR), Glioblastoma (GBM), Medulloblastoma (MB) - Group 3 (MB_Gr3), Group 4 (MB_Gr3), Group WNT (MB_WNT), Group SHH (MB_SHH) and Pilocytic Astrocytoma (PiloAstro).

r-mpfe 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MPFE
Licenses: GPL 3+
Build system: r
Synopsis: Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data
Description:

Estimate distribution of methylation patterns from a table of counts from a bisulphite sequencing experiment given a non-conversion rate and read error rate.

r-motif2site 1.14.0
Propagated dependencies: r-s4vectors@0.48.0 r-mixtools@2.0.0.1 r-mass@7.3-65 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicalignments@1.46.0 r-genomeinfodb@1.46.0 r-edger@4.8.0 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/Motif2Site
Licenses: GPL 2
Build system: r
Synopsis: Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions
Description:

Detect binding sites using motifs IUPAC sequence or bed coordinates and ChIP-seq experiments in bed or bam format. Combine/compare binding sites across experiments, tissues, or conditions. All normalization and differential steps are done using TMM-GLM method. Signal decomposition is done by setting motifs as the centers of the mixture of normal distribution curves.

Total results: 2909