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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-multirnaflow 1.8.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/loubator/MultiRNAflow
Licenses: GPL 3 FSDG-compatible
Synopsis: An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions
Description:

Our R package MultiRNAflow provides an easy to use unified framework allowing to automatically make both unsupervised and supervised (DE) analysis for datasets with an arbitrary number of biological conditions and time points. In particular, our code makes a deep downstream analysis of DE information, e.g. identifying temporal patterns across biological conditions and DE genes which are specific to a biological condition for each time.

r-mogene11stprobeset-db 8.8.0
Propagated dependencies: r-org-mm-eg-db@3.21.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mogene11stprobeset.db
Licenses: Artistic License 2.0
Synopsis: Affymetrix mogene11 annotation data (chip mogene11stprobeset)
Description:

Affymetrix mogene11 annotation data (chip mogene11stprobeset) assembled using data from public repositories.

r-mgu74aprobe 2.18.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mgu74aprobe
Licenses: LGPL 2.0+
Synopsis: Probe sequence data for microarrays of type mgu74a
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 MG-U74A\_probe\_tab.

r-multiscan 1.70.0
Propagated dependencies: r-biobase@2.68.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/multiscan
Licenses: GPL 2+
Synopsis: R package for combining multiple scans
Description:

Estimates gene expressions from several laser scans of the same microarray.

r-meat 1.22.0
Propagated dependencies: r-watermelon@2.14.0 r-tibble@3.2.1 r-summarizedexperiment@1.38.1 r-stringr@1.5.1 r-rpmm@1.25 r-minfi@1.54.1 r-impute@1.82.0 r-glmnet@4.1-8 r-dynamictreecut@1.63-1 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/sarah-voisin/MEAT
Licenses: Expat
Synopsis: Muscle Epigenetic Age Test
Description:

This package estimates epigenetic age in skeletal muscle, using DNA methylation data generated with the Illumina Infinium technology (HM27, HM450 and HMEPIC).

r-mafdb-exac-r1-0-grch38 3.10.0
Propagated dependencies: r-s4vectors@0.46.0 r-iranges@2.42.0 r-genomicscores@2.20.0 r-genomicranges@1.60.0 r-genomeinfodb@1.44.0 r-bsgenome@1.76.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MafDb.ExAC.r1.0.GRCh38
Licenses: Artistic License 2.0
Synopsis: Minor allele frequency data from ExAC release 1.0 for GRCh38
Description:

Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0) for the human genome version GRCh38.

r-mgu74cv2-db 3.13.0
Propagated dependencies: r-org-mm-eg-db@3.21.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mgu74cv2.db
Licenses: Artistic License 2.0
Synopsis: Affymetrix Affymetrix MG_U74Cv2 Array annotation data (chip mgu74cv2)
Description:

Affymetrix Affymetrix MG_U74Cv2 Array annotation data (chip mgu74cv2) assembled using data from public repositories.

r-moex10sttranscriptcluster-db 8.8.0
Propagated dependencies: r-org-mm-eg-db@3.21.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/moex10sttranscriptcluster.db
Licenses: Artistic License 2.0
Synopsis: Affymetrix moex10 annotation data (chip moex10sttranscriptcluster)
Description:

Affymetrix moex10 annotation data (chip moex10sttranscriptcluster) assembled using data from public repositories.

r-mariner 1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://ericscottdavis.com/mariner/
Licenses: Expat
Synopsis: Mariner: Explore the Hi-Cs
Description:

This package provides tools for manipulating paired ranges and working with Hi-C data in R. Functionality includes manipulating/merging paired regions, generating paired ranges, extracting/aggregating interactions from `.hic` files, and visualizing the results. Designed for compatibility with plotgardener for visualization.

r-mouse4302frmavecs 1.5.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mouse4302frmavecs
Licenses: GPL 2+
Synopsis: Vectors used by frma for microarrays of type mouse4302
Description:

This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.

r-muscle 3.52.0
Propagated dependencies: r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://www.drive5.com/muscle/
Licenses: FSDG-compatible
Synopsis: Multiple Sequence Alignment with MUSCLE
Description:

MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.

r-meigor 1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MEIGOR
Licenses: GPL 3
Synopsis: MEIGOR - MEtaheuristics for bIoinformatics Global Optimization
Description:

MEIGOR provides a comprehensive environment for performing global optimization tasks in bioinformatics and systems biology. It leverages advanced metaheuristic algorithms to efficiently search the solution space and is specifically tailored to handle the complexity and high-dimensionality of biological datasets. This package supports various optimization routines and is integrated with Bioconductor's infrastructure for a seamless analysis workflow.

r-metams 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/yguitton/metaMS
Licenses: GPL 2+
Synopsis: MS-based metabolomics annotation pipeline
Description:

MS-based metabolomics data processing and compound annotation pipeline.

r-mgu74b-db 3.13.0
Propagated dependencies: r-org-mm-eg-db@3.21.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mgu74b.db
Licenses: Artistic License 2.0
Synopsis: Affymetrix Affymetrix MG_U74B Array annotation data (chip mgu74b)
Description:

Affymetrix Affymetrix MG_U74B Array annotation data (chip mgu74b) assembled using data from public repositories.

r-miqc 1.18.0
Propagated dependencies: r-singlecellexperiment@1.30.1 r-ggplot2@3.5.2 r-flexmix@2.3-20
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/greenelab/miQC
Licenses: Modified BSD
Synopsis: Flexible, probabilistic metrics for quality control of scRNA-seq data
Description:

Single-cell RNA-sequencing (scRNA-seq) has made it possible to profile gene expression in tissues at high resolution. An important preprocessing step prior to performing downstream analyses is to identify and remove cells with poor or degraded sample quality using quality control (QC) metrics. Two widely used QC metrics to identify a ‘low-quality’ cell are (i) if the cell includes a high proportion of reads that map to mitochondrial DNA encoded genes (mtDNA) and (ii) if a small number of genes are detected. miQC is data-driven QC metric that jointly models both the proportion of reads mapping to mtDNA and the number of detected genes with mixture models in a probabilistic framework to predict the low-quality cells in a given dataset.

r-missrows 1.30.0
Propagated dependencies: r-s4vectors@0.46.0 r-plyr@1.8.9 r-multiassayexperiment@1.34.0 r-gtools@3.9.5 r-ggplot2@3.5.2
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/missRows
Licenses: Artistic License 2.0
Synopsis: Handling Missing Individuals in Multi-Omics Data Integration
Description:

The missRows package implements the MI-MFA method to deal with missing individuals ('biological units') in multi-omics data integration. The MI-MFA method generates multiple imputed datasets from a Multiple Factor Analysis model, then the yield results are combined in a single consensus solution. The package provides functions for estimating coordinates of individuals and variables, imputing missing individuals, and various diagnostic plots to inspect the pattern of missingness and visualize the uncertainty due to missing values.

r-malaria-db0 3.22.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/malaria.db0
Licenses: Artistic License 2.0
Synopsis: Base Level Annotation databases for malaria
Description:

Base annotation databases for malaria, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

r-msa2dist 1.14.0
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.2.1 r-stringr@1.5.1 r-stringi@1.8.7 r-seqinr@4.2-36 r-rlang@1.1.6 r-rcppthread@2.2.0 r-rcpp@1.0.14 r-pwalign@1.4.0 r-iranges@2.42.0 r-genomicranges@1.60.0 r-foreach@1.5.2 r-dplyr@1.1.4 r-doparallel@1.0.17 r-biostrings@2.76.0 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://gitlab.gwdg.de/mpievolbio-it/MSA2dist
Licenses: FSDG-compatible
Synopsis: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis
Description:

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calculations which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances. DNAStringSet alignments can be analysed as codon alignments to look for synonymous and nonsynonymous substitutions (dN/dS) in a parallelised fashion using a variety of substitution models. Non-aligned coding sequences can be directly used to construct pairwise codon alignments (global/local) and calculate dN/dS without any external dependencies.

r-mouse4302cdf 2.18.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mouse4302cdf
Licenses: LGPL 2.0+
Synopsis: mouse4302cdf
Description:

This package provides a package containing an environment representing the Mouse430_2.cdf file.

r-michip 1.64.0
Propagated dependencies: r-biobase@2.68.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MiChip
Licenses: GPL 2+
Synopsis: MiChip Parsing and Summarizing Functions
Description:

This package takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by otherBioConductor packages.

r-mu6500subccdf 2.18.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mu6500subccdf
Licenses: LGPL 2.0+
Synopsis: mu6500subccdf
Description:

This package provides a package containing an environment representing the Mu6500subC.CDF file.

r-nanoporernaseq 1.20.0
Propagated dependencies: r-experimenthub@2.16.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://github.com/GoekeLab/NanoporeRNASeq
Licenses: FSDG-compatible
Synopsis: Nanopore RNA-Seq Example data
Description:

The NanoporeRNASeq package contains long read RNA-Seq data generated using Oxford Nanopore Sequencing. The data consists of 6 samples from two human cell lines (K562 and MCF7) that were generated by the SG-NEx project. Each of these cell lines has three replicates, with 1 direct RNA sequencing data and 2 cDNA sequencing data. Reads are aligned to chromosome 22 (Grch38) and stored as bam files. The original data is from the SG-NEx project.

r-ncgtw 1.24.0
Propagated dependencies: r-xcms@4.6.0 r-rcpp@1.0.14 r-biocparallel@1.42.0
Channel: guix-bioc
Location: guix-bioc/packages/n.scm (guix-bioc packages n)
Home page: https://bioconductor.org/packages/ncGTW
Licenses: GPL 2
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-nadfinder 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+
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.

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