Showing 63 of total 63 results (show query)
rspatial
terra:Spatial Data Analysis
Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Maintained by Robert J. Hijmans. Last updated 2 days ago.
geospatialrasterspatialvectoronetbbprojgdalgeoscpp
559 stars 17.64 score 17k scripts 855 dependentsrspatial
raster:Geographic Data Analysis and Modeling
Reading, writing, manipulating, analyzing and modeling of spatial data. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.
Maintained by Robert J. Hijmans. Last updated 17 hours ago.
163 stars 17.23 score 58k scripts 562 dependents
bioc
SummarizedExperiment:A container (S4 class) for matrix-like assays
The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.
Maintained by Hervรฉ Pagรจs. Last updated 5 months ago.
geneticsinfrastructuresequencingannotationcoveragegenomeannotationbioconductor-packagecore-package
34 stars 16.84 score 8.6k scripts 1.2k dependentsbioc
S4Vectors:Foundation of vector-like and list-like containers in Bioconductor
The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).
Maintained by Hervรฉ Pagรจs. Last updated 2 months ago.
infrastructuredatarepresentationbioconductor-packagecore-package
18 stars 16.05 score 1.0k scripts 1.9k dependents
dankelley
oce:Analysis of Oceanographic Data
Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature. This package is discussed extensively by Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.
Maintained by Dan Kelley. Last updated 1 days ago.
146 stars 15.34 score 4.2k scripts 18 dependentsbioc
AnnotationDbi:Manipulation of SQLite-based annotations in Bioconductor
Implements a user-friendly interface for querying SQLite-based annotation data packages.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
annotationmicroarraysequencinggenomeannotationbioconductor-packagecore-package
9 stars 15.05 score 3.6k scripts 769 dependentsbioc
xcms:LC-MS and GC-MS Data Analysis
Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.
Maintained by Steffen Neumann. Last updated 14 days ago.
immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detectioncpp
196 stars 14.31 score 984 scripts 11 dependentsbioc
BiocGenerics:S4 generic functions used in Bioconductor
The package defines many S4 generic functions used in Bioconductor.
Maintained by Hervรฉ Pagรจs. Last updated 2 months ago.
infrastructurebioconductor-packagecore-package
12 stars 14.22 score 612 scripts 2.2k dependents
mhahsler
arules:Mining Association Rules and Frequent Itemsets
Provides the infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). Also provides C implementations of the association mining algorithms Apriori and Eclat. Hahsler, Gruen and Hornik (2005) <doi:10.18637/jss.v014.i15>.
Maintained by Michael Hahsler. Last updated 2 months ago.
arulesassociation-rulesfrequent-itemsets
194 stars 13.99 score 3.3k scripts 28 dependentsbioc
AnnotationHub:Client to access AnnotationHub resources
This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
infrastructuredataimportguithirdpartyclientcore-packageu24ca289073
17 stars 13.88 score 2.7k scripts 104 dependentsbioc
Gviz:Plotting data and annotation information along genomic coordinates
Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.
Maintained by Robert Ivanek. Last updated 5 months ago.
visualizationmicroarraysequencing
79 stars 13.08 score 1.4k scripts 48 dependents
ncss-tech
aqp:Algorithms for Quantitative Pedology
The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.
Maintained by Dylan Beaudette. Last updated 1 months ago.
digital-soil-mappingncss-technrcspedologypedometricssoilsoil-surveyusda
55 stars 11.90 score 1.2k scripts 2 dependentsbioc
systemPipeR:systemPipeR: Workflow Environment for Data Analysis and Report Generation
systemPipeR is a multipurpose data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by consistent sample annotation mechanisms. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates.
Maintained by Thomas Girke. Last updated 5 months ago.
geneticsinfrastructuredataimportsequencingrnaseqriboseqchipseqmethylseqsnpgeneexpressioncoveragegenesetenrichmentalignmentqualitycontrolimmunooncologyreportwritingworkflowstepworkflowmanagement
53 stars 11.52 score 344 scripts 3 dependentsbioc
VariantAnnotation:Annotation of Genetic Variants
Annotate variants, compute amino acid coding changes, predict coding outcomes.
Maintained by Bioconductor Package Maintainer. Last updated 3 months ago.
dataimportsequencingsnpannotationgeneticsvariantannotationcurlbzip2xz-utilszlib
11.39 score 1.9k scripts 152 dependentsbioc
MAST:Model-based Analysis of Single Cell Transcriptomics
Methods and models for handling zero-inflated single cell assay data.
Maintained by Andrew McDavid. Last updated 5 months ago.
geneexpressiondifferentialexpressiongenesetenrichmentrnaseqtranscriptomicssinglecell
232 stars 11.28 score 1.8k scripts 5 dependents
fmichonneau
phylobase:Base Package for Phylogenetic Structures and Comparative Data
Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.
Maintained by Francois Michonneau. Last updated 1 years ago.
18 stars 11.10 score 394 scripts 18 dependentsbioc
universalmotif:Import, Modify, and Export Motifs with R
Allows for importing most common motif types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.
Maintained by Benjamin Jean-Marie Tremblay. Last updated 5 months ago.
motifannotationmotifdiscoverydataimportgeneregulationmotif-analysismotif-enrichment-analysissequence-logocpp
28 stars 11.04 score 342 scripts 12 dependents
zdebruine
RcppML:Rcpp Machine Learning Library
Fast machine learning algorithms including matrix factorization and divisive clustering for large sparse and dense matrices.
Maintained by Zach DeBruine. Last updated 2 years ago.
clusteringmatrix-factorizationnmfrcpprcppeigensparse-matrixcppopenmp
107 stars 10.66 score 125 scripts 50 dependentsbioc
ballgown:Flexible, isoform-level differential expression analysis
Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.
Maintained by Jack Fu. Last updated 5 months ago.
immunooncologyrnaseqstatisticalmethodpreprocessingdifferentialexpression
146 stars 10.51 score 338 scripts 1 dependents
crunch-io
crunch:Crunch.io Data Tools
The Crunch.io service <https://crunch.io/> provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
Maintained by Greg Freedman Ellis. Last updated 7 days ago.
9 stars 10.47 score 200 scripts 2 dependentsbioc
Cardinal:A mass spectrometry imaging toolbox for statistical analysis
Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.
Maintained by Kylie Ariel Bemis. Last updated 3 months ago.
softwareinfrastructureproteomicslipidomicsmassspectrometryimagingmassspectrometryimmunooncologynormalizationclusteringclassificationregression
48 stars 10.32 score 200 scriptsbioc
BASiCS:Bayesian Analysis of Single-Cell Sequencing data
Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells. However, these experiments are prone to high levels of technical noise, creating new challenges for identifying genes that show genuine heterogeneous expression within the population of cells under study. BASiCS (Bayesian Analysis of Single-Cell Sequencing data) is an integrated Bayesian hierarchical model to perform statistical analyses of single-cell RNA sequencing datasets in the context of supervised experiments (where the groups of cells of interest are known a priori, e.g. experimental conditions or cell types). BASiCS performs built-in data normalisation (global scaling) and technical noise quantification (based on spike-in genes). BASiCS provides an intuitive detection criterion for highly (or lowly) variable genes within a single group of cells. Additionally, BASiCS can compare gene expression patterns between two or more pre-specified groups of cells. Unlike traditional differential expression tools, BASiCS quantifies changes in expression that lie beyond comparisons of means, also allowing the study of changes in cell-to-cell heterogeneity. The latter can be quantified via a biological over-dispersion parameter that measures the excess of variability that is observed with respect to Poisson sampling noise, after normalisation and technical noise removal. Due to the strong mean/over-dispersion confounding that is typically observed for scRNA-seq datasets, BASiCS also tests for changes in residual over-dispersion, defined by residual values with respect to a global mean/over-dispersion trend.
Maintained by Catalina Vallejos. Last updated 5 months ago.
immunooncologynormalizationsequencingrnaseqsoftwaregeneexpressiontranscriptomicssinglecelldifferentialexpressionbayesiancellbiologybioconductor-packagegene-expressionrcpprcpparmadilloscrna-seqsingle-cellopenblascppopenmp
83 stars 10.26 score 368 scripts 1 dependents
environmentalinformatics-marburg
satellite:Handling and Manipulating Remote Sensing Data
Herein, we provide a broad variety of functions which are useful for handling, manipulating, and visualizing satellite-based remote sensing data. These operations range from mere data import and layer handling (eg subsetting), over Raster* typical data wrangling (eg crop, extend), to more sophisticated (pre-)processing tasks typically applied to satellite imagery (eg atmospheric and topographic correction). This functionality is complemented by a full access to the satellite layers' metadata at any stage and the documentation of performed actions in a separate log file. Currently available sensors include Landsat 4-5 (TM), 7 (ETM+), and 8 (OLI/TIRS Combined), and additional compatibility is ensured for the Landsat Global Land Survey data set.
Maintained by Florian Detsch. Last updated 1 years ago.
22 stars 9.88 score 61 scripts 27 dependentsbioc
GenomicInteractions:Utilities for handling genomic interaction data
Utilities for handling genomic interaction data such as ChIA-PET or Hi-C, annotating genomic features with interaction information, and producing plots and summary statistics.
Maintained by Liz Ing-Simmons. Last updated 5 months ago.
softwareinfrastructuredataimportdatarepresentationhic
7 stars 9.31 score 162 scripts 5 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
4 stars 8.93 score 76 scripts 14 dependents
flr
FLCore:Core Package of FLR, Fisheries Modelling in R
Core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at <http://flr-project.org/>.
Maintained by Iago Mosqueira. Last updated 8 days ago.
fisheriesflrfisheries-modelling
16 stars 8.78 score 956 scripts 23 dependents
r-hyperspec
hyperSpec:Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)
Comfortable ways to work with hyperspectral data sets, i.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with each of the spectra. The spectra can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS, etc. More generally, any data that is recorded over a discretized variable, e.g. absorbance = f(wavelength), stored as a vector of absorbance values for discrete wavelengths is suitable.
Maintained by Claudia Beleites. Last updated 10 months ago.
data-wranglinghyperspectralimaginginfrarednmrramanspectroscopyuv-visxrf
16 stars 8.10 score 233 scripts 2 dependents
polmine
polmineR:Verbs and Nouns for Corpus Analysis
Package for corpus analysis using the Corpus Workbench ('CWB', <https://cwb.sourceforge.io>) as an efficient back end for indexing and querying large corpora. The package offers functionality to flexibly create subcorpora and to carry out basic statistical operations (count, co-occurrences etc.). The original full text of documents can be reconstructed and inspected at any time. Beyond that, the package is intended to serve as an interface to packages implementing advanced statistical procedures. Respective data structures (document-term matrices, term-co-occurrence matrices etc.) can be created based on the indexed corpora.
Maintained by Andreas Blaette. Last updated 1 years ago.
49 stars 7.96 score 311 scripts
trackage
trip:Tracking Data
Access and manipulate spatial tracking data, with straightforward coercion from and to other formats. Filter for speed and create time spent maps from tracking data. There are coercion methods to convert between 'trip' and 'ltraj' from 'adehabitatLT', and between 'trip' and 'psp' and 'ppp' from 'spatstat'. Trip objects can be created from raw or grouped data frames, and from types in the 'sp', sf', 'amt', 'trackeR', 'mousetrap', and other packages, Sumner, MD (2011) <https://figshare.utas.edu.au/articles/thesis/The_tag_location_problem/23209538>.
Maintained by Michael D. Sumner. Last updated 9 months ago.
13 stars 7.72 score 137 scripts 1 dependents
adamlilith
fasterRaster:Faster Raster and Spatial Vector Processing Using 'GRASS GIS'
Processing of large-in-memory/large-on disk rasters and spatial vectors using 'GRASS GIS' <https://grass.osgeo.org/>. Most functions in the 'terra' package are recreated. Processing of medium-sized and smaller spatial objects will nearly always be faster using 'terra' or 'sf', but for large-in-memory/large-on-disk objects, 'fasterRaster' may be faster. To use most of the functions, you must have the stand-alone version (not the 'OSGeoW4' installer version) of 'GRASS GIS' 8.0 or higher.
Maintained by Adam B. Smith. Last updated 2 days ago.
aspectdistancefragmentationfragmentation-indicesgisgrassgrass-gisrasterraster-projectionrasterizeslopetopographyvectorization
57 stars 7.68 score 8 scripts
argocanada
argoFloats:Analysis of Oceanographic Argo Floats
Supports the analysis of oceanographic data recorded by Argo autonomous drifting profiling floats. Functions are provided to (a) download and cache data files, (b) subset data in various ways, (c) handle quality-control flags and (d) plot the results according to oceanographic conventions. A shiny app is provided for easy exploration of datasets. The package is designed to work well with the 'oce' package, providing a wide range of processing capabilities that are particular to oceanographic analysis. See Kelley, Harbin, and Richards (2021) <doi:10.3389/fmars.2021.635922> for more on the scientific context and applications.
Maintained by Dan Kelley. Last updated 2 hours ago.
17 stars 7.49 score 203 scripts
ropensci
rsat:Dealing with Multiplatform Satellite Images
Downloading, customizing, and processing time series of satellite images for a region of interest. 'rsat' functions allow a unified access to multispectral images from Landsat, MODIS and Sentinel repositories. 'rsat' also offers capabilities for customizing satellite images, such as tile mosaicking, image cropping and new variables computation. Finally, 'rsat' covers the processing, including cloud masking, compositing and gap-filling/smoothing time series of images (Militino et al., 2018 <doi:10.3390/rs10030398> and Militino et al., 2019 <doi:10.1109/TGRS.2019.2904193>).
Maintained by Unai Pรฉrez - Goya. Last updated 11 months ago.
54 stars 7.45 score 52 scriptsropensci
taxlist:Handling Taxonomic Lists
Handling taxonomic lists through objects of class 'taxlist'. This package provides functions to import species lists from 'Turboveg' (<https://www.synbiosys.alterra.nl/turboveg/>) and the possibility to create backups from resulting R-objects. Also quick displays are implemented as summary-methods.
Maintained by Miguel Alvarez. Last updated 6 months ago.
12 stars 7.07 score 81 scripts 2 dependents
mschubert
narray:Subset- And Name-Aware Array Utility Functions
Stacking arrays according to dimension names, subset-aware splitting and mapping of functions, intersecting along arbitrary dimensions, converting to and from data.frames, and many other helper functions.
Maintained by Michael Schubert. Last updated 2 months ago.
27 stars 6.91 score 10 scripts 10 dependentsbioc
MotifDb:An Annotated Collection of Protein-DNA Binding Sequence Motifs
More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.
Maintained by Paul Shannon. Last updated 16 days ago.
6.86 score 404 scripts 2 dependents
thothorn
modeltools:Tools and Classes for Statistical Models
A collection of tools to deal with statistical models. The functionality is experimental and the user interface is likely to change in the future. The documentation is rather terse, but packages `coin' and `party' have some working examples. However, if you find the implemented ideas interesting we would be very interested in a discussion of this proposal. Contributions are more than welcome!
Maintained by Torsten Hothorn. Last updated 5 years ago.
6.56 score 84 scripts 254 dependentsbioc
CoreGx:Classes and Functions to Serve as the Basis for Other 'Gx' Packages
A collection of functions and classes which serve as the foundation for our lab's suite of R packages, such as 'PharmacoGx' and 'RadioGx'. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future 'Gx' suite programs. Major features include a 'CoreSet' class, from which 'RadioSet' and 'PharmacoSet' are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) <doi:10.1093/bioinformatics/btv723>. Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) <doi:10.1101/449793>.
Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.
softwarepharmacogenomicsclassificationsurvival
6.53 score 63 scripts 6 dependentsbioc
RNAmodR:Detection of post-transcriptional modifications in high throughput sequencing data
RNAmodR provides classes and workflows for loading/aggregation data from high througput sequencing aimed at detecting post-transcriptional modifications through analysis of specific patterns. In addition, utilities are provided to validate and visualize the results. The RNAmodR package provides a core functionality from which specific analysis strategies can be easily implemented as a seperate package.
Maintained by Felix G.M. Ernst. Last updated 5 months ago.
softwareinfrastructureworkflowstepvisualizationsequencingalkanilineseqbioconductormodificationsribomethseqrnarnamodr
3 stars 6.39 score 9 scripts 3 dependentsbioc
NanoStringNCTools:NanoString nCounter Tools
Tools for NanoString Technologies nCounter Technology. Provides support for reading RCC files into an ExpressionSet derived object. Also includes methods for QC and normalizaztion of NanoString data.
Maintained by Maddy Griswold. Last updated 5 months ago.
geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsmrnamicroarrayproprietaryplatformsrnaseq
6.35 score 94 scripts 4 dependents
pierreroudier
spectacles:Storing, Manipulating and Analysis Spectroscopy and Associated Data
Stores and eases the manipulation of spectra and associated data, with dedicated classes for spatial and soil-related data.
Maintained by Pierre Roudier. Last updated 2 years ago.
11 stars 6.17 score 45 scripts 1 dependents
clarahapp
funData:An S4 Class for Functional Data
S4 classes for univariate and multivariate functional data with utility functions. See <doi:10.18637/jss.v093.i05> for a detailed description of the package functionalities and its interplay with the MFPCA package for multivariate functional principal component analysis <https://CRAN.R-project.org/package=MFPCA>.
Maintained by Clara Happ-Kurz. Last updated 1 years ago.
14 stars 6.15 score 111 scripts 6 dependentsbioc
Pedixplorer:Pedigree Functions
Routines to handle family data with a Pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for Pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the Pedigree object with various criteria, and kinship for the X chromosome.
Maintained by Louis Le Nezet. Last updated 13 days ago.
softwaredatarepresentationgeneticsgraphandnetworkvisualizationkinshippedigree
2 stars 6.08 score 10 scripts
ltorgo
performanceEstimation:An Infra-Structure for Performance Estimation of Predictive Models
An infra-structure for estimating the predictive performance of predictive models. In this context, it can also be used to compare and/or select among different alternative ways of solving one or more predictive tasks. The main goal of the package is to provide a generic infra-structure to estimate the values of different metrics of predictive performance using different estimation procedures. These estimation tasks can be applied to any solutions (workflows) to the predictive tasks. The package provides easy to use standard workflows that allow the usage of any available R modeling algorithm together with some pre-defined data pre-processing steps and also prediction post- processing methods. It also provides means for addressing issues related with the statistical significance of the observed differences.
Maintained by Luis Torgo. Last updated 8 years ago.
16 stars 5.97 score 195 scripts 1 dependents
rebeccasalles
TSPred:Functions for Benchmarking Time Series Prediction
Functions for defining and conducting a time series prediction process including pre(post)processing, decomposition, modelling, prediction and accuracy assessment. The generated models and its yielded prediction errors can be used for benchmarking other time series prediction methods and for creating a demand for the refinement of such methods. For this purpose, benchmark data from prediction competitions may be used.
Maintained by Rebecca Pontes Salles. Last updated 4 years ago.
benchmarkinglinear-modelsmachine-learningnonstationaritytime-series-forecasttime-series-prediction
24 stars 5.53 score 94 scripts 1 dependents
icosa-grid
icosa:Global Triangular and Penta-Hexagonal Grids Based on Tessellated Icosahedra
Implementation of icosahedral grids in three dimensions. The spherical-triangular tessellation can be set to create grids with custom resolutions. Both the primary triangular and their inverted penta-hexagonal grids can be calculated. Additional functions are provided that allow plotting of the grids and associated data, the interaction of the grids with other raster and vector objects, and treating the grids as a graphs.
Maintained by Adam T. Kocsis. Last updated 7 months ago.
4 stars 5.41 score 65 scripts
simonmoulds
lulcc:Land Use Change Modelling in R
Classes and methods for spatially explicit land use change modelling in R.
Maintained by Simon Moulds. Last updated 5 years ago.
41 stars 5.37 score 38 scriptsbioc
ASpli:Analysis of Alternative Splicing Using RNA-Seq
Integrative pipeline for the analysis of alternative splicing using RNAseq.
Maintained by Ariel Chernomoretz. Last updated 5 months ago.
immunooncologygeneexpressiontranscriptionalternativesplicingcoveragedifferentialexpressiondifferentialsplicingtimecoursernaseqgenomeannotationsequencingalignment
5.33 score 45 scripts 1 dependents
mmrabe
designr:Balanced Factorial Designs
Generate balanced factorial designs with crossed and nested random and fixed effects <https://github.com/mmrabe/designr>.
Maintained by Maximilian M. Rabe. Last updated 2 years ago.
10 stars 5.18 score 15 scripts
alphaprime7
normfluodbf:Cleans and Normalizes FLUOstar DBF and DAT Files from 'Liposome' Flux Assays
Cleans and Normalizes FLUOstar DBF and DAT Files obtained from liposome flux assays. Users should verify extended usage of the package on files from other assay types.
Maintained by Tingwei Adeck. Last updated 5 months ago.
1 stars 4.98 score 12 scripts
pchausse
momentfit:Methods of Moments
Several classes for moment-based models are defined. The classes are defined for moment conditions derived from a single equation or a system of equations. The conditions can also be expressed as functions or formulas. Several methods are also offered to facilitate the development of different estimation techniques. The methods that are currently provided are the Generalized method of moments (Hansen 1982; <doi:10.2307/1912775>), for single equations and systems of equation, and the Generalized Empirical Likelihood (Smith 1997; <doi:10.1111/j.0013-0133.1997.174.x>, Kitamura 1997; <doi:10.1214/aos/1069362388>, Newey and Smith 2004; <doi:10.1111/j.1468-0262.2004.00482.x>, and Anatolyev 2005 <doi:10.1111/j.1468-0262.2005.00601.x>).
Maintained by Pierre Chausse. Last updated 1 years ago.
4.80 score 21 scripts 1 dependents
fatelarico
FinNet:Quickly Build and Manipulate Financial Networks
Providing classes, methods, and functions to deal with financial networks. Users can easily store information about both physical and legal persons by using pre-made classes that are studied for integration with scraping packages such as 'rvest' and 'RSelenium'. Moreover, the package assists in creating various types of financial networks depending on the type of relation between its units depending on the relation under scrutiny (ownership, board interlocks, etc.), the desired tie type (valued or binary), and renders them in the most common formats (adjacency matrix, incidence matrix, edge list, 'igraph', 'network'). There are also ad-hoc functions for the Fiedler value, global network efficiency, and cascade-failure analysis.
Maintained by Fabio Ashtar Telarico. Last updated 5 months ago.
2 stars 4.78 score 7 scriptsbioc
immunoClust:immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
immunoClust is a model based clustering approach for Flow Cytometry samples. The cell-events of single Flow Cytometry samples are modelled by a mixture of multinominal normal- or t-distributions. The cell-event clusters of several samples are modelled by a mixture of multinominal normal-distributions aiming stable co-clusters across these samples.
Maintained by Till Soerensen. Last updated 8 days ago.
clusteringflowcytometrysinglecellcellbasedassaysimmunooncologygslcpp
4.41 score 4 scriptsbioc
PDATK:Pancreatic Ductal Adenocarcinoma Tool-Kit
Pancreatic ductal adenocarcinoma (PDA) has a relatively poor prognosis and is one of the most lethal cancers. Molecular classification of gene expression profiles holds the potential to identify meaningful subtypes which can inform therapeutic strategy in the clinical setting. The Pancreatic Cancer Adenocarcinoma Tool-Kit (PDATK) provides an S4 class-based interface for performing unsupervised subtype discovery, cross-cohort meta-clustering, gene-expression-based classification, and subsequent survival analysis to identify prognostically useful subtypes in pancreatic cancer and beyond. Two novel methods, Consensus Subtypes in Pancreatic Cancer (CSPC) and Pancreatic Cancer Overall Survival Predictor (PCOSP) are included for consensus-based meta-clustering and overall-survival prediction, respectively. Additionally, four published subtype classifiers and three published prognostic gene signatures are included to allow users to easily recreate published results, apply existing classifiers to new data, and benchmark the relative performance of new methods. The use of existing Bioconductor classes as input to all PDATK classes and methods enables integration with existing Bioconductor datasets, including the 21 pancreatic cancer patient cohorts available in the MetaGxPancreas data package. PDATK has been used to replicate results from Sandhu et al (2019) [https://doi.org/10.1200/cci.18.00102] and an additional paper is in the works using CSPC to validate subtypes from the included published classifiers, both of which use the data available in MetaGxPancreas. The inclusion of subtype centroids and prognostic gene signatures from these and other publications will enable researchers and clinicians to classify novel patient gene expression data, allowing the direct clinical application of the classifiers included in PDATK. Overall, PDATK provides a rich set of tools to identify and validate useful prognostic and molecular subtypes based on gene-expression data, benchmark new classifiers against existing ones, and apply discovered classifiers on novel patient data to inform clinical decision making.
Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.
geneexpressionpharmacogeneticspharmacogenomicssoftwareclassificationsurvivalclusteringgeneprediction
1 stars 4.31 score 17 scripts
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 9 months ago.
7 stars 4.23 score 49 scripts
reidt03
RadOnc:Analytical Tools for Radiation Oncology
Designed for the import, analysis, and visualization of dosimetric and volumetric data in Radiation Oncology, the tools herein enable import of dose-volume histogram information from multiple treatment planning system platforms and 3D structural representations and dosimetric information from 'DICOM-RT' files. These tools also enable subsequent visualization and statistical analysis of these data.
Maintained by Reid F. Thompson. Last updated 2 months ago.
8 stars 3.78 score 19 scripts
lawremi
rsolr:R to Solr Interface
A comprehensive R API for querying Apache Solr databases. A Solr core is represented as a data frame or list that supports Solr-side filtering, sorting, transformation and aggregation, all through the familiar base R API. Queries are processed lazily, i.e., a query is only sent to the database when the data are required.
Maintained by Michael Lawrence. Last updated 3 years ago.
9 stars 3.65 score 6 scripts
soroushmdg
gwid:Genome-Wide Identity-by-Descent
Methods and tools for the analysis of Genome Wide Identity-by-Descent ('gwid') mapping data, focusing on testing whether there is a higher occurrence of Identity-By-Descent (IBD) segments around potential causal variants in cases compared to controls, which is crucial for identifying rare variants. To enhance its analytical power, 'gwid' incorporates a Sliding Window Approach, allowing for the detection and analysis of signals from multiple Single Nucleotide Polymorphisms (SNPs).
Maintained by Soroush Mahmoudiandehkordi. Last updated 7 months ago.
1 stars 3.60 score 4 scripts
sergioventurini
dmbc:Model Based Clustering of Binary Dissimilarity Measurements
Functions for fitting a Bayesian model for grouping binary dissimilarity matrices in homogeneous clusters. Currently, it includes methods only for binary data (<doi:10.18637/jss.v100.i16>).
Maintained by Sergio Venturini. Last updated 6 months ago.
2 stars 3.30 score 4 scripts
adamkocsis
via:Virtual Arrays
The base class 'VirtualArray' is defined, which acts as a wrapper around lists allowing users to fold arbitrary sequential data into n-dimensional, R-style virtual arrays. The derived 'XArray' class is defined to be used for homogeneous lists that contain a single class of objects. The 'RasterArray' and 'SfArray' classes enable the use of stacked spatial data instead of lists.
Maintained by Adam T. Kocsis. Last updated 2 years ago.
3 stars 3.18 score 8 scripts
r-forge
pems.utils:Portable Emissions (and Other Mobile) Measurement System Utilities
Utility functions for the handling, analysis and visualisation of data from portable emissions measurement systems ('PEMS') and other similar mobile activity monitoring devices. The package includes a dedicated 'pems' data class that manages many of the quality control, unit handling and data archiving issues that can hinder efforts to standardise 'PEMS' research.
Maintained by Karl Ropkins. Last updated 3 months ago.
3.06 score 19 scripts
tim-salabim
remote:Empirical Orthogonal Teleconnections in R
Empirical orthogonal teleconnections in R. 'remote' is short for 'R(-based) EMpirical Orthogonal TEleconnections'. It implements a collection of functions to facilitate empirical orthogonal teleconnection analysis. Empirical Orthogonal Teleconnections (EOTs) denote a regression based approach to decompose spatio-temporal fields into a set of independent orthogonal patterns. They are quite similar to Empirical Orthogonal Functions (EOFs) with EOTs producing less abstract results. In contrast to EOFs, which are orthogonal in both space and time, EOT analysis produces patterns that are orthogonal in either space or time.
Maintained by Tim Appelhans. Last updated 9 years ago.
2.79 score 100 scripts
cran
arulesSequences:Mining Frequent Sequences
Add-on for arules to handle and mine frequent sequences. Provides interfaces to the C++ implementation of cSPADE by Mohammed J. Zaki.
Maintained by Christian Buchta. Last updated 7 months ago.
12 stars 2.63 scorecran
crops:Changepoints for a Range of Penalties (CROPS)
Implements the Changepoints for a Range of Penalties (CROPS) algorithm of Haynes et al. (2017) <doi:10.1080/10618600.2015.1116445> for finding all of the optimal segmentations for multiple penalty values over a continuous range.
Maintained by Daniel Grose. Last updated 3 years ago.
1.48 score 1 dependents