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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-covrna 1.36.0
Propagated dependencies: r-genefilter@1.92.0 r-biobase@2.70.0 r-ade4@1.7-23
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/covRNA
Licenses: GPL 2+
Build system: r
Synopsis: Multivariate Analysis of Transcriptomic Data
Description:

This package provides the analysis methods fourthcorner and RLQ analysis for large-scale transcriptomic data.

r-carnival 2.20.0
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.3.0 r-stringr@1.6.0 r-rmarkdown@2.30 r-rjson@0.2.23 r-readr@2.1.6 r-lpsolve@5.6.23 r-igraph@2.2.1 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/saezlab/CARNIVAL
Licenses: GPL 3
Build system: r
Synopsis: CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
Description:

An upgraded causal reasoning tool from Melas et al in R with updated assignments of TFs weights from PROGENy scores. Optimization parameters can be freely adjusted and multiple solutions can be obtained and aggregated.

r-curatedadiporna 1.26.0
Propagated dependencies: r-summarizedexperiment@1.40.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/MahShaaban/curatedAdipoRNA
Licenses: GPL 3
Build system: r
Synopsis: Curated RNA-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)
Description:

This package provides a curated dataset of RNA-Seq samples. The samples are MDI-induced pre-phagocytes (3T3-L1) at different time points/stage of differentiation. The package document the data collection, pre-processing and processing. In addition to the documentation, the package contains the scripts that was used to generated the data.

r-chipsim 1.64.0
Propagated dependencies: r-xvector@0.50.0 r-shortread@1.68.0 r-iranges@2.44.0 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/ChIPsim
Licenses: GPL 2+
Build system: r
Synopsis: Simulation of ChIP-seq experiments
Description:

This package provides a general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.

r-cellity 1.38.0
Propagated dependencies: r-topgo@2.62.0 r-robustbase@0.99-6 r-org-mm-eg-db@3.22.0 r-org-hs-eg-db@3.22.0 r-mvoutlier@2.1.1 r-ggplot2@4.0.1 r-e1071@1.7-16 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cellity
Licenses: GPL 2+
Build system: r
Synopsis: Quality Control for Single-Cell RNA-seq Data
Description:

This package provides a support vector machine approach to identifying and filtering low quality cells from single-cell RNA-seq datasets.

r-cardinalio 1.8.0
Propagated dependencies: r-s4vectors@0.48.0 r-ontologyindex@2.12 r-matter@2.12.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: http://www.cardinalmsi.org
Licenses: Artistic License 2.0 FSDG-compatible
Build system: r
Synopsis: Read and write mass spectrometry imaging files
Description:

Fast and efficient reading and writing of mass spectrometry imaging data files. Supports imzML and Analyze 7.5 formats. Provides ontologies for mass spectrometry imaging.

r-crisprverse 1.12.0
Propagated dependencies: r-rlang@1.1.6 r-crisprviz@1.12.0 r-crisprscoredata@1.14.0 r-crisprscore@1.14.0 r-crisprdesign@1.12.0 r-crisprbowtie@1.14.0 r-crisprbase@1.14.0 r-cli@3.6.5 r-biocmanager@1.30.27
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/crisprVerse/crisprVerse
Licenses: Expat
Build system: r
Synopsis: Easily install and load the crisprVerse ecosystem for CRISPR gRNA design
Description:

The crisprVerse is a modular ecosystem of R packages developed for the design and manipulation of CRISPR guide RNAs (gRNAs). All packages share a common language and design principles. This package is designed to make it easy to install and load the crisprVerse packages in a single step. To learn more about the crisprVerse, visit <https://www.github.com/crisprVerse>.

r-cogaps 3.30.0
Propagated dependencies: r-testthat@3.3.0 r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-s4vectors@0.48.0 r-rhdf5@2.54.0 r-rcpp@1.1.0 r-rcolorbrewer@1.1-3 r-gplots@3.2.0 r-ggplot2@4.0.1 r-forcats@1.0.1 r-fgsea@1.36.0 r-dplyr@1.1.4 r-cluster@2.1.8.1 r-biocparallel@1.44.0 r-bh@1.87.0-1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CoGAPS
Licenses: Modified BSD
Build system: r
Synopsis: Coordinated Gene Activity in Pattern Sets
Description:

Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.

r-coseq 1.34.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-rmixmod@2.1.10 r-mvtnorm@1.3-3 r-htsfilter@1.50.0 r-htscluster@2.0.11 r-ggplot2@4.0.1 r-edger@4.8.0 r-e1071@1.7-16 r-deseq2@1.50.2 r-corrplot@0.95 r-compositions@2.0-9 r-capushe@1.1.3 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/coseq
Licenses: GPL 3
Build system: r
Synopsis: Co-Expression Analysis of Sequencing Data
Description:

Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.

r-cexor 1.48.0
Propagated dependencies: r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rsamtools@2.26.0 r-rcolorbrewer@1.1-3 r-iranges@2.44.0 r-idr@1.3 r-genomicranges@1.62.0 r-genomation@1.42.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/pmb59/CexoR
Licenses: Artistic License 2.0 FSDG-compatible
Build system: r
Synopsis: An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
Description:

Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Then, irreproducible discovery rate for overlapping peak-pairs across biological replicates is computed.

r-cogps 1.54.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/coGPS
Licenses: GPL 2
Build system: r
Synopsis: cancer outlier Gene Profile Sets
Description:

Gene Set Enrichment Analysis of P-value based statistics for outlier gene detection in dataset merged from multiple studies.

r-cardinal 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-protgenerics@1.42.0 r-nlme@3.1-168 r-matter@2.12.0 r-matrix@1.7-4 r-irlba@2.3.5.1 r-ebimage@4.52.0 r-cardinalio@1.8.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: http://www.cardinalmsi.org
Licenses: Artistic License 2.0 FSDG-compatible
Build system: r
Synopsis: mass spectrometry imaging toolbox for statistical analysis
Description:

This package implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.

r-celegans-db 3.13.0
Propagated dependencies: r-org-ce-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/celegans.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix Celegans Array annotation data (chip celegans)
Description:

Affymetrix Affymetrix Celegans Array annotation data (chip celegans) assembled using data from public repositories.

r-cancerclass 1.54.0
Propagated dependencies: r-biobase@2.70.0 r-binom@1.1-1.1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cancerclass
Licenses: FSDG-compatible
Build system: r
Synopsis: Development and validation of diagnostic tests from high-dimensional molecular data
Description:

The classification protocol starts with a feature selection step and continues with nearest-centroid classification. The accurarcy of the predictor can be evaluated using training and test set validation, leave-one-out cross-validation or in a multiple random validation protocol. Methods for calculation and visualization of continuous prediction scores allow to balance sensitivity and specificity and define a cutoff value according to clinical requirements.

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

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

r-compran 1.18.0
Propagated dependencies: r-venndiagram@1.7.3 r-tidyr@1.3.1 r-tibble@3.3.0 r-stringr@1.6.0 r-shinyjs@2.1.0 r-shinydashboard@0.7.3 r-shiny@1.11.1 r-scales@1.4.0 r-rlang@1.1.6 r-rio@1.2.4 r-rcolorbrewer@1.1-3 r-purrr@1.2.0 r-magrittr@2.0.4 r-ggplot2@4.0.1 r-forcats@1.0.1 r-dt@0.34.0 r-dplyr@1.1.4 r-data-table@1.17.8
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-clomial 1.46.0
Propagated dependencies: r-permute@0.9-8 r-matrixstats@1.5.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/Clomial
Licenses: GPL 2+
Build system: r
Synopsis: Infers clonal composition of a tumor
Description:

Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor.

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
Propagated dependencies: r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-rcy3@2.30.0 r-rcpparmadillo@15.2.2-1 r-rcpp@1.1.0 r-network@1.19.0 r-matrix@1.7-4 r-igraph@2.2.1 r-ggrepel@0.9.6 r-ggpubr@0.6.2 r-ggplot2@4.0.1 r-ggnetwork@0.5.14 r-ggally@2.4.0 r-genomictools-filehandler@0.1.5.9 r-dplyr@1.1.4 r-deseq2@1.50.2 r-complexheatmap@2.26.0 r-clusterprofiler@4.18.2 r-circlize@0.4.16
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-chipanalyser 1.32.0
Propagated dependencies: r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rocr@1.0-11 r-rcpproll@0.3.1 r-rcolorbrewer@1.1-3 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocmanager@1.30.27
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-cll 1.50.0
Propagated dependencies: r-biobase@2.70.0 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CLL
Licenses: LGPL 2.0+
Build system: r
Synopsis: Package for CLL Gene Expression Data
Description:

The CLL package contains the chronic lymphocytic leukemia (CLL) gene expression data. The CLL data had 24 samples that were either classified as progressive or stable in regards to disease progression. The data came from Dr. Sabina Chiaretti at Division of Hematology, Department of Cellular Biotechnologies and Hematology, University La Sapienza, Rome, Italy and Dr. Jerome Ritz at Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.

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-cnvgsa 1.54.0
Propagated dependencies: r-splitstackshape@1.4.8 r-genomicranges@1.62.0 r-foreach@1.5.2 r-doparallel@1.0.17 r-brglm@0.7.3
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cnvGSA
Licenses: LGPL 2.0+
Build system: r
Synopsis: Gene Set Analysis of (Rare) Copy Number Variants
Description:

This package is intended to facilitate gene-set association with rare CNVs in case-control studies.

r-cntools 1.66.0
Propagated dependencies: r-genefilter@1.92.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CNTools
Licenses: LGPL 2.0+
Build system: r
Synopsis: Convert segment data into a region by sample matrix to allow for other high level computational analyses
Description:

This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data.

r-chromdraw 2.40.0
Propagated dependencies: r-rcpp@1.1.0 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: www.plantcytogenomics.org/chromDraw
Licenses: GPL 3
Build system: r
Synopsis: chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion
Description:

ChromDraw is a R package for drawing the schemes of karyotype(s) in the linear and circular fashion. It is possible to visualized cytogenetic marsk on the chromosomes. This tool has own input data format. Input data can be imported from the GenomicRanges data structure. This package can visualized the data in the BED file format. Here is requirement on to the first nine fields of the BED format. Output files format are *.eps and *.svg.

Total results: 2909