Showing 42 of total 42 results (show query)
ropensci
taxize:Taxonomic Information from Around the Web
Interacts with a suite of web application programming interfaces (API) for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. Some of the services supported include 'NCBI E-utilities' (<https://www.ncbi.nlm.nih.gov/books/NBK25501/>), 'Encyclopedia of Life' (<https://eol.org/docs/what-is-eol/data-services>), 'Global Biodiversity Information Facility' (<https://techdocs.gbif.org/en/openapi/>), and many more. Links to the API documentation for other supported services are available in the documentation for their respective functions in this package.
Maintained by Zachary Foster. Last updated 11 days ago.
taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperbiodiversitydarwincoredatataxize
10.0 match 274 stars 13.63 score 1.6k scripts 23 dependentsropensci
ritis:Integrated Taxonomic Information System Client
An interface to the Integrated Taxonomic Information System ('ITIS') (<https://www.itis.gov>). Includes functions to work with the 'ITIS' REST API methods (<https://www.itis.gov/ws_description.html>), as well as the 'Solr' web service (<https://www.itis.gov/solr_documentation.html>).
Maintained by Julia Blum. Last updated 1 months ago.
taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperitistaxize
10.0 match 16 stars 7.72 score 64 scripts 24 dependentsropensci
nuts:Convert European Regional Data
Motivated by changing administrative boundaries over time, the 'nuts' package can convert European regional data with NUTS codes between versions (2006, 2010, 2013, 2016 and 2021) and levels (NUTS 1, NUTS 2 and NUTS 3). The package uses spatial interpolation as in Lam (1983) <doi:10.1559/152304083783914958> based on granular (100m x 100m) area, population and land use data provided by the European Commission's Joint Research Center.
Maintained by Moritz Hennicke. Last updated 5 months ago.
europeeuropean-unioneurostatnomenclaturenutsnuts-codesnuts-regionsregional-data
10.0 match 8 stars 5.86 score 3 scripts
dboslab
expowo:An R package for mining global plant diversity and distribution data
Produces diversity estimates and species lists with associated global distribution for any vascular plant family and genus from 'Plants of the World Online' database <https://powo.science.kew.org/>, by interacting with the source code of each plant taxon page. It also creates global maps of species richness, graphics of species discoveries and nomenclatural changes over time. For more details
Maintained by Debora Zuanny. Last updated 5 months ago.
6.7 match 8 stars 7.36 score 64 scripts
hiweller
recolorize:Color-Based Image Segmentation
Automatic, semi-automatic, and manual functions for generating color maps from images. The idea is to simplify the colors of an image according to a metric that is useful for the user, using deterministic methods whenever possible. Many images will be clustered well using the out-of-the-box functions, but the package also includes a toolbox of functions for making manual adjustments (layer merging/isolation, blurring, fitting to provided color clusters or those from another image, etc). Also includes export methods for other color/pattern analysis packages (pavo, patternize, colordistance).
Maintained by Hannah Weller. Last updated 12 days ago.
5.9 match 39 stars 7.68 score 87 scripts
bioc
rgoslin:Lipid Shorthand Name Parsing and Normalization
The R implementation for the Grammar of Succint Lipid Nomenclature parses different short hand notation dialects for lipid names. It normalizes them to a standard name. It further provides calculated monoisotopic masses and sum formulas for each successfully parsed lipid name and supplements it with LIPID MAPS Category and Class information. Also, the structural level and further structural details about the head group, fatty acyls and functional groups are returned, where applicable.
Maintained by Nils Hoffmann. Last updated 5 months ago.
softwarelipidomicsmetabolomicspreprocessingnormalizationmassspectrometrycpp
4.9 match 5 stars 5.64 score 22 scripts
rjake
simplecolors:Access Color Names Using a Standardized Nomenclature
A curated set of colors that are called using a standardized syntax: saturation + hue + lightness. For example, "brightblue4" and "mutedred2". Functions exists to return individual colors by name or to build palettes across or within hues. Most functions allow you to visualize the palettes in addition to returning the desired hex codes.
Maintained by Jake Riley. Last updated 2 years ago.
4.6 match 14 stars 5.78 score 87 scripts
lgnbhl
I14Y:Search and Get Data from the I14Y Interoperability Platform of Switzerland
Search and download Swiss data and metadata from the I14Y interoperability platform of Switzerland using its public APIs <https://www.i14y.admin.ch/api/index.html>.
Maintained by Felix Luginbuhl. Last updated 10 days ago.
7.8 match 3.30 score
thinkr-open
inca3:Donnees De L'Etude INCA 3
Données de consommations et habitudes alimentaires de l'étude INCA 3. Carine Dubuisson, Ariane Dufour, Sandrine Carrillo, Peggy Drouillet-Pinard, Sabrina Havard, Jean-Luc Volatier (2019). The Third French Individual and National Food Consumption (INCA3) Survey 2014-2015: method, design and participation rate in the framework of a European harmonization process. Public Health Nutrition: 22(4), 584–600. (doi:10.1017/S1368980018002896).
Maintained by Vincent Guyader. Last updated 3 years ago.
hacktoberfestthinkr-not-maintained
6.0 match 5 stars 3.88 score 4 scriptsropensci
tradestatistics:Open Trade Statistics API Wrapper and Utility Program
Access 'Open Trade Statistics' API from R to download international trade data.
Maintained by Mauricio Vargas. Last updated 7 months ago.
api-wrapperdata-tableinternational-tradejsonliteopen-trade-statistics
3.2 match 77 stars 7.15 score 92 scripts
ethan-young
multitool:Run Multiverse Style Analyses
Run the same analysis over a range of arbitrary data processing decisions. 'multitool' provides an interface for creating alternative analysis pipelines and turning them into a grid of all possible pipelines. Using this grid as a blueprint, you can model your data across all possible pipelines and summarize the results.
Maintained by Ethan Young. Last updated 4 months ago.
3.8 match 1 stars 5.93 score 71 scriptsbioc
Modstrings:Working with modified nucleotide sequences
Representing nucleotide modifications in a nucleotide sequence is usually done via special characters from a number of sources. This represents a challenge to work with in R and the Biostrings package. The Modstrings package implements this functionallity for RNA and DNA sequences containing modified nucleotides by translating the character internally in order to work with the infrastructure of the Biostrings package. For this the ModRNAString and ModDNAString classes and derivates and functions to construct and modify these objects despite the encoding issues are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.
Maintained by Felix G.M. Ernst. Last updated 5 months ago.
dataimportdatarepresentationinfrastructuresequencingsoftwarebioconductorbiostringsdnadna-modificationsmodified-nucleotidesnucleotidesrnarna-modification-alphabetrna-modificationssequences
3.0 match 1 stars 6.64 score 5 scripts 8 dependents
josempozo
zoolog:Zooarchaeological Analysis with Log-Ratios
Includes functions and reference data to generate and manipulate log-ratios (also known as log size index (LSI) values) from measurements obtained on zooarchaeological material. Log ratios are used to compare the relative (rather than the absolute) dimensions of animals from archaeological contexts (Meadow 1999, ISBN: 9783896463883). zoolog is also able to seamlessly integrate data and references with heterogeneous nomenclature, which is internally managed by a zoolog thesaurus. A preliminary version of the zoolog methods was first used by Trentacoste, Nieto-Espinet, and Valenzuela-Lamas (2018) <doi:10.1371/journal.pone.0208109>.
Maintained by Jose M Pozo. Last updated 3 years ago.
4.1 match 6 stars 4.48 score 4 scripts
bioc
SPIAT:Spatial Image Analysis of Tissues
SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.
Maintained by Yuzhou Feng. Last updated 2 days ago.
biomedicalinformaticscellbiologyspatialclusteringdataimportimmunooncologyqualitycontrolsinglecellsoftwarevisualization
2.0 match 22 stars 8.59 score 69 scripts
danielebizzarri
MiMIR:Metabolomics-Based Models for Imputing Risk
Provides an intuitive framework for ad-hoc statistical analysis of 1H-NMR metabolomics by Nightingale Health. It allows to easily explore new metabolomics measurements assayed by Nightingale Health, comparing the distributions with a large Consortium (BBMRI-nl); project previously published metabolic scores [<doi:10.1016/j.ebiom.2021.103764>, <doi:10.1161/CIRCGEN.119.002610>, <doi:10.1038/s41467-019-11311-9>, <doi:10.7554/eLife.63033>, <doi:10.1161/CIRCULATIONAHA.114.013116>, <doi:10.1007/s00125-019-05001-w>]; and calibrate the metabolic surrogate values to a desired dataset.
Maintained by Daniele Bizzarri. Last updated 2 years ago.
binary-risk-factorsbiomarkerslinear-regressionmetabolitesmetabolomicsnightingale-metabolomicsrisk-factor-modelsrisk-factorssurrogate-models
4.0 match 8 stars 4.11 score 32 scriptsbioc
MeSHDbi:DBI to construct MeSH-related package from sqlite file
The package is unified implementation of MeSH.db, MeSH.AOR.db, and MeSH.PCR.db and also is interface to construct Gene-MeSH package (MeSH.XXX.eg.db). loadMeSHDbiPkg import sqlite file and generate MeSH.XXX.eg.db.
Maintained by Koki Tsuyuzaki. Last updated 5 months ago.
annotationannotationdatainfrastructure
3.0 match 4.76 score 32 scripts 3 dependentsropensci
rusda:Interface to USDA Databases
An interface to the web service methods provided by the United States Department of Agriculture (USDA). The Agricultural Research Service (ARS) provides a large set of databases. The current version of the package holds interfaces to the Systematic Mycology and Microbiology Laboratory (SMML), which consists of four databases: Fungus-Host Distributions, Specimens, Literature and the Nomenclature database. It provides functions for querying these databases. The main function is \code{associations}, which allows searching for fungus-host combinations.
Maintained by Franz-Sebastian Krah. Last updated 4 years ago.
4.0 match 14 stars 3.54 score 5 scripts
usepa
tcpl:ToxCast Data Analysis Pipeline
The ToxCast Data Analysis Pipeline ('tcpl') is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, 'invitrodb'. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but 'tcpl' can be used to support diverse chemical screening efforts.
Maintained by Jason Brown. Last updated 2 days ago.
1.5 match 36 stars 9.41 score 90 scriptsbioc
immApex:Tools for Adaptive Immune Receptor Sequence-Based Machine and Deep Learning
A set of tools to build tensorflow/keras3-based models in R from amino acid and nucleotide sequences focusing on adaptive immune receptors. The package includes pre-processing of sequences, unifying gene nomenclature usage, encoding sequences, and combining models. This package will serve as the basis of future immune receptor sequence functions/packages/models compatible with the scRepertoire ecosystem.
Maintained by Nick Borcherding. Last updated 19 days ago.
softwareimmunooncologysinglecellclassificationannotationsequencingmotifannotation
2.2 match 8 stars 5.92 score 3 scripts
fcampelo
MOEADr:Component-Wise MOEA/D Implementation
Modular implementation of Multiobjective Evolutionary Algorithms based on Decomposition (MOEA/D) [Zhang and Li (2007), <DOI:10.1109/TEVC.2007.892759>] for quick assembling and testing of new algorithmic components, as well as easy replication of published MOEA/D proposals. The full framework is documented in a paper published in the Journal of Statistical Software [<doi:10.18637/jss.v092.i06>].
Maintained by Felipe Campelo. Last updated 2 years ago.
moeadmultiobjective-optimization
2.0 match 20 stars 6.30 score 40 scriptsbioc
MetMashR:Metabolite Mashing with R
A package to merge, filter sort, organise and otherwise mash together metabolite annotation tables. Metabolite annotations can be imported from multiple sources (software) and combined using workflow steps based on S4 class templates derived from the `struct` package. Other modular workflow steps such as filtering, merging, splitting, normalisation and rest-api queries are included.
Maintained by Gavin Rhys Lloyd. Last updated 5 months ago.
2.0 match 2 stars 5.81 score 5 scriptsbioc
ontoProc:processing of ontologies of anatomy, cell lines, and so on
Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies.
Maintained by Vincent Carey. Last updated 2 days ago.
infrastructuregobioinformaticsgenomicsontology
1.7 match 3 stars 6.37 score 75 scripts 2 dependents
mpadge
spatialcluster:R port of redcap
R port of redcap (Regionalization with dynamically constrained agglomerative clustering and partitioning).
Maintained by Mark Padgham. Last updated 2 months ago.
clusterclustering-algorithmspatialcpp
2.0 match 31 stars 4.97 score 1 scripts
fbellelli
countries:Deal with Country Data in an Easy Way
Wrangle country data more effectively and quickly. This package contains functions to easily identify and convert country names, download country information, merge country data from different sources, and make quick world maps.
Maintained by Francesco Saverio Bellelli. Last updated 22 days ago.
1.7 match 3 stars 5.15 score 47 scripts
robinhankin
frab:How to Add Two R Tables
Methods to "add" two R tables; also an alternative interpretation of named vectors as generalized R tables, so that c(a=1,b=2,c=3) + c(b=3,a=-1) will return c(b=5,c=3). Uses 'disordR' discipline (Hankin, 2022, <doi:10.48550/arXiv.2210.03856>). Extraction and replacement methods are provided. The underlying mathematical structure is the Free Abelian group, hence the name. To cite in publications please use Hankin (2023) <doi:10.48550/arXiv.2307.13184>.
Maintained by Robin K. S. Hankin. Last updated 3 months ago.
1.5 match 1 stars 5.26 score 1 dependentsbioc
GA4GHclient:A Bioconductor package for accessing GA4GH API data servers
GA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.
Maintained by Welliton Souza. Last updated 5 months ago.
datarepresentationthirdpartyclient
1.8 match 1 stars 4.48 score 3 scripts 1 dependents
pascoalf
ulrb:Unsupervised Learning Based Definition of Microbial Rare Biosphere
A tool to define rare biosphere. 'ulrb' solves the problem of the definition of rarity by replacing arbitrary thresholds with an unsupervised machine learning algorithm (partitioning around medoids, or k-medoids). This algorithm works for any type of microbiome data, provided there is a species abundance table. For validation of this method to different species abundance tables see Pascoal et al, 2024 (in peer-review). This method also works for non-microbiome data.
Maintained by Francisco Pascoal. Last updated 19 days ago.
1.3 match 3 stars 5.68 score 9 scriptsbioc
CHRONOS:CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
A package used for efficient unraveling of the inherent dynamic properties of pathways. MicroRNA-mediated subpathway topologies are extracted and evaluated by exploiting the temporal transition and the fold change activity of the linked genes/microRNAs.
Maintained by Panos Balomenos. Last updated 5 months ago.
systemsbiologygraphandnetworkpathwayskeggopenjdk
1.9 match 3.86 score 12 scriptsbioc
MSstatsLiP:LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.
Maintained by Devon Kohler. Last updated 5 months ago.
immunooncologymassspectrometryproteomicssoftwaredifferentialexpressiononechanneltwochannelnormalizationqualitycontrolcpp
1.3 match 7 stars 5.62 score 5 scripts
computationalproteomics
proteoDeconv:Enabling Cell-Type Deconvolution of Proteomics Data
Tools for deconvoluting proteomics data to identify and quantify cell types (e.g., immune cell types) in complex biological samples.
Maintained by Måns Zamore. Last updated 1 days ago.
1.7 match 2 stars 3.85 scorebioc
immunotation:Tools for working with diverse immune genes
MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells. The repertoire of antigens presented in a given genetic background largely depends on the sequence of the encoded MHC molecules, and thus, in humans, on the highly variable HLA (human leukocyte antigen) genes of the hyperpolymorphic HLA locus. More than 28,000 different HLA alleles have been reported, with significant differences in allele frequencies between human populations worldwide. Reproducible and consistent annotation of HLA alleles in large-scale bioinformatics workflows remains challenging, because the available reference databases and software tools often use different HLA naming schemes. The package immunotation provides tools for consistent annotation of HLA genes in typical immunoinformatics workflows such as for example the prediction of MHC-presented peptides in different human donors. Converter functions that provide mappings between different HLA naming schemes are based on the MHC restriction ontology (MRO). The package also provides automated access to HLA alleles frequencies in worldwide human reference populations stored in the Allele Frequency Net Database.
Maintained by Katharina Imkeller. Last updated 5 months ago.
softwareimmunooncologybiomedicalinformaticsgeneticsannotation
1.3 match 8 stars 4.90 score 3 scripts
cb4ds
DGEobj:Differential Gene Expression (DGE) Analysis Results Data Object
Provides a flexible container to manage and annotate Differential Gene Expression (DGE) analysis results (Smythe et. al (2015) <doi:10.1093/nar/gkv007>). The DGEobj has data slots for row (gene), col (samples), assays (matrix n-rows by m-samples dimensions) and metadata (not keyed to row, col, or assays). A set of accessory functions to deposit, query and retrieve subsets of a data workflow has been provided. Attributes are used to capture metadata such as species and gene model, including reproducibility information such that a 3rd party can access a DGEobj history to see how each data object was created or modified. Since the DGEobj is customizable and extensible it is not limited to RNA-seq analysis types of workflows -- it can accommodate nearly any data analysis workflow that starts from a matrix of assays (rows) by samples (columns).
Maintained by Connie Brett. Last updated 2 months ago.
1.2 match 2 stars 5.60 score 33 scripts 2 dependents
cran
ensembleTax:Ensemble Taxonomic Assignments of Amplicon Sequencing Data
Creates ensemble taxonomic assignments of amplicon sequencing data in R using outputs of multiple taxonomic assignment algorithms and/or reference databases. Includes flexible algorithms for mapping taxonomic nomenclatures onto one another and for computing ensemble taxonomic assignments.
Maintained by Dylan Catlett. Last updated 4 years ago.
2.2 match 2.48 score 7 scripts
sjmack
HLAtools:Toolkit for HLA Immunogenomics
A toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA 'GitHub' repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods.
Maintained by Steven Mack. Last updated 12 days ago.
0.5 match 4 stars 6.21 score 7 scripts 1 dependents
bioc
ipdDb:IPD IMGT/HLA and IPD KIR database for Homo sapiens
All alleles from the IPD IMGT/HLA <https://www.ebi.ac.uk/ipd/imgt/hla/> and IPD KIR <https://www.ebi.ac.uk/ipd/kir/> database for Homo sapiens. Reference: Robinson J, Maccari G, Marsh SGE, Walter L, Blokhuis J, Bimber B, Parham P, De Groot NG, Bontrop RE, Guethlein LA, and Hammond JA KIR Nomenclature in non-human species Immunogenetics (2018), in preparation.
Maintained by Steffen Klasberg. Last updated 5 months ago.
genomicvariationsequencematchingvariantannotationdatarepresentationannotationhubsoftware
0.5 match 3.30 score 4 scriptscran
harmonizer:Harmonizing CN8 and PC8 Product Codes
Several functions are provided to harmonize CN8 (Combined Nomenclature 8 digits) and PC8 (Production Communautaire 8 digits) product codes over time and the classification systems HS6 and BEC. Harmonization of CN8 codes are possible by default from 1995 to 2022 and of PC8 from 2001 to 2021, respectively.
Maintained by Christoph Baumgartner. Last updated 2 years ago.
0.5 match 2.70 score 6 scripts
peyronlab
aliases2entrez:Converts Human gene symbols to entrez IDs
Queries multiple resources authors HGNC (2019) <https://www.genenames.org>, authors limma (2015) <doi:10.1093/nar/gkv007> to find the correspondence between evolving nomenclature of human gene symbols, aliases, previous symbols or synonyms with stable, curated gene entrezID from NCBI database. This allows fast, accurate and up-to-date correspondence between human gene expression datasets from various date and platform (e.g: gene symbol: BRCA1 - ID: 672).
Maintained by Raphael Bonnet. Last updated 4 years ago.
0.5 match 1 stars 2.00 score 10 scripts