Showing 55 of total 55 results (show query)
neotomadb
neotoma2:Working with the Neotoma Paleoecology Database
Access and manipulation of data using the Neotoma Paleoecology Database. <https://api.neotomadb.org/api-docs/>.
Maintained by Dominguez Vidana Socorro. Last updated 8 months ago.
earthcubeneotomansfpaleoecology
54.5 match 8 stars 5.35 score 56 scripts
ropensci
rvertnet:Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Retrieve, map and summarize data from the 'VertNet.org' archives (<https://vertnet.org/>). Functions allow searching by many parameters, including 'taxonomic' names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large 'datasets' via email.
Maintained by Dave Slager. Last updated 5 months ago.
speciesoccurrencesbiodiversitymapsvertnetmammalsmammaliaspecimensapi-wrapperspecimenspocc
23.9 match 7 stars 8.51 score 35 scripts 6 dependents
geomorphr
geomorph:Geometric Morphometric Analyses of 2D and 3D Landmark Data
Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.
Maintained by Dean Adams. Last updated 1 months ago.
13.0 match 76 stars 12.05 score 700 scripts 6 dependents
idigbio
ridigbio:Interface to the iDigBio Data API
An interface to iDigBio's search API that allows downloading specimen records. Searches are returned as a data.frame. Other functions such as the metadata end points return lists of information. iDigBio is a US project focused on digitizing and serving museum specimen collections on the web. See <https://www.idigbio.org> for information on iDigBio.
Maintained by Jesse Bennett. Last updated 4 days ago.
15.3 match 16 stars 10.23 score 63 scripts 7 dependentsropensci
rgbif:Interface to the Global Biodiversity Information Facility API
A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/developer/summary>). GBIF is a database of species occurrence records from sources all over the globe. rgbif includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, getting counts of occurrence records, and using the GBIF tile map service to make rasters summarizing huge amounts of data.
Maintained by John Waller. Last updated 3 days ago.
gbifspecimensapiweb-servicesoccurrencesspeciestaxonomybiodiversitydatalifewatchoscibiospocc
10.0 match 161 stars 13.26 score 2.1k scripts 20 dependents
cran
compositions:Compositional Data Analysis
Provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by J. Aitchison and V. Pawlowsky-Glahn.
Maintained by K. Gerald van den Boogaart. Last updated 1 years ago.
18.1 match 1 stars 6.35 score 36 dependentsropensci
spocc:Interface to Species Occurrence Data Sources
A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'iNaturalist', 'eBird', Integrated Digitized 'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes functionality for retrieving species occurrence data, and combining those data.
Maintained by Hannah Owens. Last updated 1 months ago.
specimensapiweb-servicesoccurrencesspeciestaxonomygbifinatvertnetebirdidigbioobisalaantwebbisondataecoengineinaturalistoccurrencespecies-occurrencespocc
10.0 match 118 stars 10.09 score 552 scripts 5 dependents
luomus
finbif:Interface for the 'Finnish Biodiversity Information Facility' API
A programmatic interface to the 'Finnish Biodiversity Information Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates Finnish biodiversity data from multiple sources in a single open access portal for researchers, citizen scientists, industry and government. 'FinBIF' allows users of biodiversity information to find, access, combine and visualise data on Finnish plants, animals and microorganisms. The 'finbif' package makes the publicly available data in 'FinBIF' easily accessible to programmers. Biodiversity information is available on taxonomy and taxon occurrence. Occurrence data can be filtered by taxon, time, location and other variables. The data accessed are conveniently preformatted for subsequent analyses.
Maintained by William K. Morris. Last updated 6 days ago.
apibiodiversitybiodiversity-informaticsbiodiversity-informationfinbiffinbif-accessoccurrencesr-programmingspeciesspecimenstaxontaxonomyweb-services
10.0 match 5 stars 8.15 score 42 scripts 3 dependents
mindthegap-erc
StratPal:Stratigraphic Paleobiology Modeling Pipelines
The fossil record is a joint expression of ecological, taphonomic, evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012, ISBN:978-0226649382). This package allowing to simulate biological processes in the time domain (e.g., trait evolution, fossil abundance), and examine how their expression in the rock record (stratigraphic domain) is influenced based on age-depth models, ecological niche models, and taphonomic effects. Functions simulating common processes used in modeling trait evolution or event type data such as first/last occurrences are provided and can be used standalone or as part of a pipeline. The package comes with example data sets and tutorials in several vignettes, which can be used as a template to set up one's own simulation.
Maintained by Niklas Hohmann. Last updated 24 days ago.
palaeobiologypalaeontologypaleobiologypaleontologystratigraphic-paleobiologystratigraphy
9.6 match 1 stars 5.88 score 18 scripts
pharmaverse
pharmaversesdtm:SDTM Test Data for the 'Pharmaverse' Family of Packages
A set of Study Data Tabulation Model (SDTM) datasets from the Clinical Data Interchange Standards Consortium (CDISC) pilot project used for testing and developing Analysis Data Model (ADaM) datasets inside the pharmaverse family of packages. SDTM dataset specifications are described in the CDISC SDTM implementation guide, accessible by creating a free account on <https://www.cdisc.org/>.
Maintained by Edoardo Mancini. Last updated 2 days ago.
7.3 match 15 stars 7.40 score 143 scriptsropensci
occCite:Querying and Managing Large Biodiversity Occurrence Datasets
Facilitates the gathering of biodiversity occurrence data from disparate sources. Metadata is managed throughout the process to facilitate reporting and enhanced ability to repeat analyses.
Maintained by Hannah L. Owens. Last updated 5 months ago.
biodiversity-databiodiversity-informaticsbiodiversity-standardscitationsmuseum-collection-specimensmuseum-collectionsmuseum-metadata
6.7 match 23 stars 7.30 score 43 scriptsropensci
paleobioDB:Download and Process Data from the Paleobiology Database
Includes functions to wrap most endpoints of the 'PaleobioDB' API and functions to visualize and process the fossil data. The API documentation for the Paleobiology Database can be found at <https://paleobiodb.org/data1.2/>.
Maintained by Adrián Castro Insua. Last updated 1 years ago.
7.3 match 42 stars 6.19 score 74 scriptsropensci
bold:Interface to Bold Systems API
A programmatic interface to the Web Service methods provided by Bold Systems (<http://www.boldsystems.org/>) for genetic 'barcode' data. Functions include methods for searching by sequences by taxonomic names, ids, collectors, and institutions; as well as a function for searching for specimens, and downloading trace files.
Maintained by Salix Dubois. Last updated 3 months ago.
biodiversitybarcodednasequencesfastaapi-wrapperbarcodestaxize
6.0 match 18 stars 5.74 score 57 scripts
tathey
VLF:Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records
Using frequency matrices, very low frequency variants (VLFs) are assessed for amino acid and nucleotide sequences. The VLFs are then compared to see if they occur in only one member of a species, singleton VLFs, or if they occur in multiple members of a species, shared VLFs. The amino acid and nucleotide VLFs are then compared to see if they are concordant with one another. Amino acid VLFs are also assessed to determine if they lead to a change in amino acid residue type, and potential changes to protein structures. Based on Stoeckle and Kerr (2012) <doi:10.1371/journal.pone.0043992>.
Maintained by Taryn B. T. Athey. Last updated 3 years ago.
15.9 match 2.16 score 48 scripts 1 dependents
zarquon42b
Morpho:Calculations and Visualisations Related to Geometric Morphometrics
A toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.
Maintained by Stefan Schlager. Last updated 5 months ago.
3.4 match 51 stars 10.00 score 218 scripts 13 dependents
psolymos
EDMAinR:Euclidean Distance Matrix Analysis in R
A coordinate-free approach for comparing biological shapes using landmark data based on Lele and Richtsmeier (1991) <doi:10.1002/ajpa.1330860307>.
Maintained by Peter Solymos. Last updated 2 years ago.
comparing-biological-shapescoordinate-freelandmark-datamorphometricsmultivariate-statistics
8.7 match 3 stars 3.78 score 9 scripts
sciencegraph
brinton:A Graphical EDA Tool
An automated graphical exploratory data analysis (EDA) tool that introduces: a.) wideplot graphics for exploring the structure of a dataset through a grid of variables and graphic types. b.) longplot graphics, which present the entire catalog of available graphics for representing a particular variable using a grid of graphic types and variations on these types. c.) plotup function, which presents a particular graphic for a specific variable of a dataset. The plotup() function also makes it possible to obtain the code used to generate the graphic, meaning that the user can adjust its properties as needed. d.) matrixplot graphics that is a grid of a particular graphic showing bivariate relationships between all pairs of variables of a certain(s) type(s) in a multivariate data set.
Maintained by Pere Millán-Martínez. Last updated 2 years ago.
5.3 match 15 stars 4.95 score 12 scripts
pharmaverse
admiralvaccine:Vaccine Extension Package for ADaM in 'R' Asset Library
Programming vaccine specific Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in 'R'. Flat model is followed as per Center for Biologics Evaluation and Research (CBER) guidelines for creating vaccine specific domains. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team (2021), <https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>). The package is an extension package of the 'admiral' package.
Maintained by Sukalpo Saha. Last updated 2 months ago.
3.4 match 6 stars 7.44 score 23 scriptsropensci
SymbiotaR2:Downloading Data from Symbiota2 Portals into R
Download data from Symbiota2 portals using Symbiota's API. Covers the Checklists, Collections, Crowdsource, Exsiccati, Glossary, ImageProcessor, Key, Media, Occurrence, Reference, Taxa, Traits, and UserRoles API families. Each Symbiota2 portal owner can load their own plugins (and modified code), and so this package may not cover every possible API endpoint from a given Symbiota2 instance.
Maintained by Austin Koontz. Last updated 3 years ago.
databaselibraryspecimen-recordssymbiotasymbiota2symbiota2-portal
7.5 match 2 stars 3.30 score 4 scripts
jessica-arbour
LOST:Missing Morphometric Data Simulation and Estimation
Functions for simulating missing morphometric data randomly, with taxonomic bias and with anatomical bias. LOST also includes functions for estimating linear and geometric morphometric data.
Maintained by J. Arbour. Last updated 2 months ago.
10.2 match 2.30 score 4 scripts
tim-tu
weibulltools:Statistical Methods for Life Data Analysis
Provides statistical methods and visualizations that are often used in reliability engineering. Comprises a compact and easily accessible set of methods and visualization tools that make the examination and adjustment as well as the analysis and interpretation of field data (and bench tests) as simple as possible. Non-parametric estimators like Median Ranks, Kaplan-Meier (Abernethy, 2006, <ISBN:978-0-9653062-3-2>), Johnson (Johnson, 1964, <ISBN:978-0444403223>), and Nelson-Aalen for failure probability estimation within samples that contain failures as well as censored data are included. The package supports methods like Maximum Likelihood and Rank Regression, (Genschel and Meeker, 2010, <DOI:10.1080/08982112.2010.503447>) for the estimation of multiple parametric lifetime distributions, as well as the computation of confidence intervals of quantiles and probabilities using the delta method related to Fisher's confidence intervals (Meeker and Escobar, 1998, <ISBN:9780471673279>) and the beta-binomial confidence bounds. If desired, mixture model analysis can be done with segmented regression and the EM algorithm. Besides the well-known Weibull analysis, the package also contains Monte Carlo methods for the correction and completion of imprecisely recorded or unknown lifetime characteristics. (Verband der Automobilindustrie e.V. (VDA), 2016, <ISSN:0943-9412>). Plots are created statically ('ggplot2') or interactively ('plotly') and can be customized with functions of the respective visualization package. The graphical technique of probability plotting as well as the addition of regression lines and confidence bounds to existing plots are supported.
Maintained by Tim-Gunnar Hensel. Last updated 2 years ago.
field-data-analysisinteractive-visualizationsplotlyreliability-analysisweibull-analysisweibulltoolsopenblascpp
3.6 match 13 stars 6.15 score 54 scripts
alexbhatt
epidm:UK Epidemiological Data Management
Contains utilities and functions for the cleaning, processing and management of patient level public health data for surveillance and analysis held by the UK Health Security Agency, UKHSA.
Maintained by Alex Bhattacharya. Last updated 7 months ago.
4.0 match 13 stars 5.07 score 2 scripts
sacema
inctools:Incidence Estimation Tools
Tools for estimating incidence from biomarker data in cross- sectional surveys, and for calibrating tests for recent infection. Implements and extends the method of Kassanjee et al. (2012) <doi:10.1097/EDE.0b013e3182576c07>.
Maintained by Eduard Grebe. Last updated 4 years ago.
biomarkersbiostatisticsepidemiologyhivincidenceincidence-estimationincidence-inferenceinfectious-diseasesstatistics
3.1 match 6 stars 6.51 score 27 scripts
timcdlucas
paleomorph:Geometric Morphometric Tools for Paleobiology
Fill missing symmetrical data with mirroring, calculate Procrustes alignments with or without scaling, and compute standard or vector correlation and covariance matrices (congruence coefficients) of 3D landmarks. Tolerates missing data for all analyses.
Maintained by Tim Lucas. Last updated 8 years ago.
morphometricspaleobiologyprocrustesstatistical-analysis
4.9 match 4 stars 3.60 score 20 scripts
zsteinmetz
envalysis:Miscellaneous Functions for Environmental Analyses
Small toolbox for data analyses in environmental chemistry and ecotoxicology. Provides, for example, calibration() to calculate calibration curves and corresponding limits of detection (LODs) and limits of quantification (LOQs) according to German DIN 32645 (2008). texture() makes it easy to estimate soil particle size distributions from hydrometer measurements (ASTM D422-63, 2007).
Maintained by Zacharias Steinmetz. Last updated 5 months ago.
analyticschemistryecotoxicologyenvironmentsoil
2.2 match 8 stars 6.30 score 83 scripts
sybig
RPPanalyzer:Reads, Annotates, and Normalizes Reverse Phase Protein Array Data
Reads in sample description and slide description files and annotates the expression values taken from GenePix results files (text file format used by many microarray scanner and software providers). After normalization data can be visualized as boxplot, heatmap or dotplot.
Maintained by Torsten Schoeps. Last updated 1 years ago.
3.4 match 1 stars 3.63 score 71 scripts
bimanc
PopulationGrowthR:Linear Population Growth Scenarios
Fit linear splines to species time series to detect population growth scenarios based on Hyndman, R J and Mesgaran, M B and Cousens, R D (2015) <doi:10.1007/s10530-015-0962-8>.
Maintained by Biman Chakraborty. Last updated 3 years ago.
11.4 match 1.00 score 2 scripts
mreginato
monographaR:Taxonomic Monographs Tools
Contains functions intended to facilitate the production of plant taxonomic monographs. The package includes functions to convert tables into taxonomic descriptions, lists of collectors, examined specimens, identification keys (dichotomous and interactive), and can generate a monograph skeleton. Additionally, wrapper functions to batch the production of phenology histograms and distributional and diversity maps are also available.
Maintained by Marcelo Reginato. Last updated 1 years ago.
2.4 match 3 stars 4.73 score 18 scripts
liamkendall
pollimetry:Estimate Pollinator Body Size and Co-Varying Ecological Traits
Tools to estimate pollinator body size and co-varying traits. This package contains novel Bayesian predictive models of pollinator body size (for bees and hoverflies) and bee foraging range, as well as preexisting predictive models for pollinator body size (currently implemented for ants, bees, butterflies, flies, moths and wasps), bee tongue length, foraging range, total field nectar loads and wing loading. An additional GitHub repository <https://github.com/liamkendall/pollimetrydata> provides model objects to use the bodysize and foraging.range functions internally. All models are described in Kendall et al. (2019) <doi:10.1002/ece3.4835> & Kendall et al. (2022) <doi:TBC>.
Maintained by Liam Kendall. Last updated 2 years ago.
3.3 match 3 stars 3.26 score 12 scripts
nataliepatten
gatoRs:Geographic and Taxonomic Occurrence R-Based Scrubbing
Streamlines downloading and cleaning biodiversity data from Integrated Digitized Biocollections (iDigBio) and the Global Biodiversity Information Facility (GBIF).
Maintained by Natalie N. Patten. Last updated 10 months ago.
1.8 match 11 stars 6.16 score 66 scripts
markbells
geoscale:Geological Time Scale Plotting
Functionality for adding the geological timescale to bivariate plots.
Maintained by Mark A. Bell. Last updated 3 years ago.
3.6 match 1 stars 2.80 score 26 scripts 4 dependentsropensci
EndoMineR:Functions to mine endoscopic and associated pathology datasets
This script comprises the functions that are used to clean up endoscopic reports and pathology reports as well as many of the scripts used for analysis. The scripts assume the endoscopy and histopathology data set is merged already but it can also be used of course with the unmerged datasets.
Maintained by Sebastian Zeki. Last updated 7 months ago.
endoscopygastroenterologypeer-reviewedsemi-structured-datatext-mining
1.8 match 13 stars 5.47 score 30 scripts
mjbutrim
dilp:Reconstruct Paleoclimate and Paleoecology with Leaf Physiognomy
Use leaf physiognomic methods to reconstruct mean annual temperature (MAT), mean annual precipitation (MAP), and leaf dry mass per area (Ma), along with other useful quantitative leaf traits. Methods in this package described in Lowe et al. (in review).
Maintained by Matthew J. Butrim. Last updated 10 months ago.
2.0 match 4.54 score 2 scripts
robinhankin
ResistorArray:Electrical Properties of Resistor Networks
Electrical properties of resistor networks using matrix methods.
Maintained by Robin K. S. Hankin. Last updated 1 years ago.
2.0 match 4.32 score 14 scripts 1 dependents
kamapu
vegtable:Handling Vegetation Data Sets
Import and handling data from vegetation-plot databases, especially data stored in 'Turboveg 2' (<https://www.synbiosys.alterra.nl/turboveg/>). Also import/export routines for exchange of data with 'Juice' (<https://www.sci.muni.cz/botany/juice/>) are implemented.
Maintained by Miguel Alvarez. Last updated 8 months ago.
2.0 match 7 stars 4.23 score 49 scriptsropensci
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.
2.2 match 14 stars 3.54 score 5 scripts
bioc
MultiAssayExperiment:Software for the integration of multi-omics experiments in Bioconductor
Harmonize data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.
Maintained by Marcel Ramos. Last updated 2 months ago.
infrastructuredatarepresentationbioconductorbioconductor-packagegenomicsnci-itcrtcgau24ca289073
0.5 match 71 stars 14.95 score 670 scripts 127 dependents
blakedickson
Morphoscape:Computation and Visualization of Adaptive Landscapes
Implements adaptive landscape methods first described by Polly et al. (2016) <doi:10.1080/02724634.2016.1111225> for the integration, analysis and visualization of biological trait data on a phenotypic morphospace - typically defined by shape metrics.
Maintained by Blake Dickson. Last updated 9 months ago.
1.2 match 4 stars 5.56 score 8 scriptscran
MiDA:Microarray Data Analysis
Set of functions designed to simplify transcriptome analysis and identification of marker molecules using microarrays data. The package includes a set of functions that allows performing full pipeline of analysis including data normalization, summarisation, binary classification, FDR (False Discovery Rate) multiple comparison and the definition of potential biological markers.
Maintained by Elena Filatova. Last updated 6 years ago.
4.5 match 1.08 score 12 scriptscran
molaR:Dental Surface Complexity Measurement Tools
Surface topography calculations of Dirichlet's normal energy, relief index, surface slope, and orientation patch count for teeth using scans of enamel caps. Importantly, for the relief index and orientation patch count calculations to work, the scanned tooth files must be oriented with the occlusal plane parallel to the x and y axes, and perpendicular to the z axis. The files should also be simplified, and smoothed in some other software prior to uploading into R.
Maintained by James D. Pampush. Last updated 2 years ago.
1.8 match 1 stars 2.68 score 16 scripts 1 dependentsbioc
RaggedExperiment:Representation of Sparse Experiments and Assays Across Samples
This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns. The RaggedExperiment class derives from a GRangesList representation and provides a semblance of a rectangular dataset.
Maintained by Marcel Ramos. Last updated 4 months ago.
infrastructuredatarepresentationcopynumbercore-packagedata-structuremutationsu24ca289073
0.5 match 4 stars 8.96 score 76 scripts 15 dependents
peter-t-ruehr
forceR:Force Measurement Analyses
For cleaning and analysis of graphs, such as animal closing force measurements. 'forceR' was initially written and optimized to deal with insect bite force measurements, but can be used for any time series. Includes a full workflow to load, plot and crop data, correct amplifier and baseline drifts, identify individual peak shapes (bites), rescale (normalize) peak curves, and find best polynomial fits to describe and analyze force curve shapes.
Maintained by Peter T. Rühr. Last updated 12 months ago.
1.2 match 3.70 score 10 scriptsbioc
metabCombiner:Method for Combining LC-MS Metabolomics Feature Measurements
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.
Maintained by Hani Habra. Last updated 5 months ago.
softwaremassspectrometrymetabolomicsmass-spectrometry
0.5 match 10 stars 5.65 score 5 scriptsbioc
smoppix:Analyze Single Molecule Spatial Omics Data Using the Probabilistic Index
Test for univariate and bivariate spatial patterns in spatial omics data with single-molecule resolution. The tests implemented allow for analysis of nested designs and are automatically calibrated to different biological specimens. Tests for aggregation, colocalization, gradients and vicinity to cell edge or centroid are provided.
Maintained by Stijn Hawinkel. Last updated 27 days ago.
transcriptomicsspatialsinglecellcpp
0.5 match 1 stars 5.18 score 4 scripts
jphill01
HACSim:Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment
Performs iterative extrapolation of species' haplotype accumulation curves using a nonparametric stochastic (Monte Carlo) optimization method for assessment of specimen sampling completeness based on the approach of Phillips et al. (2015) <doi:10.1515/dna-2015-0008>, Phillips et al. (2019) <doi:10.1002/ece3.4757> and Phillips et al. (2020) <doi: 10.7717/peerj-cs.243>. 'HACSim' outputs a number of useful summary statistics of sampling coverage ("Measures of Sampling Closeness"), including an estimate of the likely required sample size (along with desired level confidence intervals) necessary to recover a given number/proportion of observed unique species' haplotypes. Any genomic marker can be targeted to assess likely required specimen sample sizes for genetic diversity assessment. The method is particularly well-suited to assess sampling sufficiency for DNA barcoding initiatives. Users can also simulate their own DNA sequences according to various models of nucleotide substitution. A Shiny app is also available.
Maintained by Jarrett D. Phillips. Last updated 6 months ago.
dna-barcodinghaplotype-accumulation-curvescpp
0.8 match 3.48 score 5 scripts
boopsboops
spider:Species Identity and Evolution in R
Analysis of species limits and DNA barcoding data. Included are functions for generating important summary statistics from DNA barcode data, assessing specimen identification efficacy, testing and optimizing divergence threshold limits, assessment of diagnostic nucleotides, and calculation of the probability of reciprocal monophyly. Additionally, a sliding window function offers opportunities to analyse information across a gene, often used for marker design in degraded DNA studies. Further information on the package has been published in Brown et al (2012) <doi:10.1111/j.1755-0998.2011.03108.x>.
Maintained by Rupert A. Collins. Last updated 6 years ago.
dna-barcodeednaevolutionspecies-delimitationspecies-identity
0.5 match 2 stars 5.20 score 66 scripts 1 dependents
charvey23
AvInertia:Calculate the Inertial Properties of a Flying Bird
Tools to compute the center of gravity and moment of inertia tensor of any flying bird. The tools function by modeling a bird as a composite structure of simple geometric objects. This requires detailed morphological measurements of bird specimens although those obtained for the associated paper have been included in the package for use. Refer to the vignettes and supplementary material for detailed information on the package function.
Maintained by Christina Harvey. Last updated 3 years ago.
0.5 match 6 stars 5.00 score 33 scriptsbioc
spiky:Spike-in calibration for cell-free MeDIP
spiky implements methods and model generation for cfMeDIP (cell-free methylated DNA immunoprecipitation) with spike-in controls. CfMeDIP is an enrichment protocol which avoids destructive conversion of scarce template, making it ideal as a "liquid biopsy," but creating certain challenges in comparing results across specimens, subjects, and experiments. The use of synthetic spike-in standard oligos allows diagnostics performed with cfMeDIP to quantitatively compare samples across subjects, experiments, and time points in both relative and absolute terms.
Maintained by Tim Triche. Last updated 5 months ago.
differentialmethylationdnamethylationnormalizationpreprocessingqualitycontrolsequencing
0.5 match 2 stars 4.90 score 3 scripts
eahouseman
OxyBS:Processing of Oxy-Bisulfite Microarray Data
Provides utilities for processing of Oxy-Bisulfite microarray data (e.g. via the Illumina Infinium platform, <http://www.illumina.com>) with tandem arrays, one using conventional bisulfite conversion, the other using oxy-bisulfite conversion.
Maintained by E. Andres Houseman. Last updated 8 years ago.
1.9 match 1.08 score 12 scripts
aprofico
Arothron:Geometric Morphometric Methods and Virtual Anthropology Tools
Tools for geometric morphometric analysis. The package includes tools of virtual anthropology to align two not articulated parts belonging to the same specimen, to build virtual cavities as endocast (Profico et al, 2021 <doi:10.1002/ajpa.24340>).
Maintained by Antonio Profico. Last updated 2 years ago.
0.5 match 2.59 score 13 scripts 2 dependents
