close

Showing 89 of total 89 results (show query)

bioc

Biostrings:Efficient manipulation of biological strings

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Maintained by Hervé Pagès. Last updated 1 months ago.

sequencematchingalignmentsequencinggeneticsdataimportdatarepresentationinfrastructurebioconductor-packagecore-package

62 stars 17.77 score 8.6k scripts 1.2k dependents

bioc

GenomicRanges:Representation and manipulation of genomic intervals

The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.

Maintained by Hervé Pagès. Last updated 4 months ago.

geneticsinfrastructuredatarepresentationsequencingannotationgenomeannotationcoveragebioconductor-packagecore-package

44 stars 17.68 score 13k scripts 1.3k dependents

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 dependents

rspatial

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 This package has been superseded by the "terra" package 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.

cpp

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 Hervé Pagès. Last updated 5 months ago.

geneticsinfrastructuresequencingannotationcoveragegenomeannotationbioconductor-packagecore-package

34 stars 16.84 score 8.6k scripts 1.2k dependents

bioc

GenomeInfoDb:Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

Maintained by Hervé Pagès. Last updated 2 months ago.

geneticsdatarepresentationannotationgenomeannotationbioconductor-packagecore-package

32 stars 16.32 score 1.3k scripts 1.7k dependents

bioc

IRanges:Foundation of integer range manipulation in Bioconductor

Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.

Maintained by Hervé Pagès. Last updated 2 months ago.

infrastructuredatarepresentationbioconductor-packagecore-package

22 stars 16.09 score 2.1k scripts 1.8k dependents

bioc

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 Hervé Pagès. Last updated 2 months ago.

infrastructuredatarepresentationbioconductor-packagecore-package

18 stars 16.05 score 1.0k scripts 1.9k dependents

bioc

DelayedArray:A unified framework for working transparently with on-disk and in-memory array-like datasets

Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, ordinary arrays and, data frames.

Maintained by Hervé Pagès. Last updated 1 months ago.

infrastructuredatarepresentationannotationgenomeannotationbioconductor-packagecore-packageu24ca289073

27 stars 15.59 score 538 scripts 1.2k dependents

bioc

GenomicAlignments:Representation and manipulation of short genomic alignments

Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

Maintained by Hervé Pagès. Last updated 5 months ago.

infrastructuredataimportgeneticssequencingrnaseqsnpcoveragealignmentimmunooncologybioconductor-packagecore-package

10 stars 15.21 score 3.1k scripts 528 dependents

bioc

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 dependents

bioc

BiocGenerics:S4 generic functions used in Bioconductor

The package defines many S4 generic functions used in Bioconductor.

Maintained by Hervé Pagès. Last updated 2 months ago.

infrastructurebioconductor-packagecore-package

12 stars 14.22 score 612 scripts 2.2k dependents

bioc

BSgenome:Software infrastructure for efficient representation of full genomes and their SNPs

Infrastructure shared by all the Biostrings-based genome data packages.

Maintained by Hervé Pagès. Last updated 2 months ago.

geneticsinfrastructuredatarepresentationsequencematchingannotationsnpbioconductor-packagecore-package

9 stars 14.12 score 1.2k scripts 267 dependents

ropensci

git2r:Provides Access to Git Repositories

Interface to the 'libgit2' library, which is a pure C implementation of the 'Git' core methods. Provides access to 'Git' repositories to extract data and running some basic 'Git' commands.

Maintained by Stefan Widgren. Last updated 14 hours ago.

gitgit-clientlibgit2libgit2-library

218 stars 13.93 score 836 scripts 46 dependents

bioc

rtracklayer:R interface to genome annotation files and the UCSC genome browser

Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.

Maintained by Michael Lawrence. Last updated 3 days ago.

annotationvisualizationdataimportzlibopensslcurl

12.66 score 6.7k scripts 480 dependents

data-cleaning

validate:Data Validation Infrastructure

Declare data validation rules and data quality indicators; confront data with them and analyze or visualize the results. The package supports rules that are per-field, in-record, cross-record or cross-dataset. Rules can be automatically analyzed for rule type and connectivity. Supports checks implied by an SDMX DSD file as well. See also Van der Loo and De Jonge (2018) <doi:10.1002/9781118897126>, Chapter 6 and the JSS paper (2021) <doi:10.18637/jss.v097.i10>.

Maintained by Mark van der Loo. Last updated 24 days ago.

data-cleaningvalidation

419 stars 12.39 score 448 scripts 8 dependents

bioc

TFBSTools:Software Package for Transcription Factor Binding Site (TFBS) Analysis

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

Maintained by Ge Tan. Last updated 16 days ago.

motifannotationgeneregulationmotifdiscoverytranscriptionalignment

28 stars 12.36 score 1.1k scripts 18 dependents

alexiosg

rugarch:Univariate GARCH Models

ARFIMA, in-mean, external regressors and various GARCH flavors, with methods for fit, forecast, simulation, inference and plotting.

Maintained by Alexios Galanos. Last updated 3 months ago.

cpp

26 stars 12.13 score 1.3k scripts 15 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 dependents

bioc

destiny:Creates diffusion maps

Create and plot diffusion maps.

Maintained by Philipp Angerer. Last updated 4 months ago.

cellbiologycellbasedassaysclusteringsoftwarevisualizationdiffusion-mapsdimensionality-reductioncpp

82 stars 11.44 score 792 scripts 1 dependents

bioc

XVector:Foundation of external vector representation and manipulation in Bioconductor

Provides memory efficient S4 classes for storing sequences "externally" (e.g. behind an R external pointer, or on disk).

Maintained by Hervé Pagès. Last updated 3 months ago.

infrastructuredatarepresentationbioconductor-packagecore-packagezlib

2 stars 11.36 score 67 scripts 1.7k dependents

pik-piam

magclass:Data Class and Tools for Handling Spatial-Temporal Data

Data class for increased interoperability working with spatial-temporal data together with corresponding functions and methods (conversions, basic calculations and basic data manipulation). The class distinguishes between spatial, temporal and other dimensions to facilitate the development and interoperability of tools build for it. Additional features are name-based addressing of data and internal consistency checks (e.g. checking for the right data order in calculations).

Maintained by Jan Philipp Dietrich. Last updated 22 days ago.

5 stars 11.16 score 412 scripts 56 dependents

bioc

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

bioc

S4Arrays:Foundation of array-like containers in Bioconductor

The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides: (1) low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and (2) a framework that facilitates block processing of array-like objects (typically on-disk objects).

Maintained by Hervé Pagès. Last updated 2 months ago.

infrastructuredatarepresentationbioconductor-packagecore-package

5 stars 10.99 score 8 scripts 1.2k dependents

metrumresearchgroup

mrgsolve:Simulate from ODE-Based Models

Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

Maintained by Kyle T Baron. Last updated 9 days ago.

mrgsolveodeopenblascpp

138 stars 10.90 score 1.2k scripts 3 dependents

r-forge

surveillance:Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

Statistical methods for the modeling and monitoring of time series of counts, proportions and categorical data, as well as for the modeling of continuous-time point processes of epidemic phenomena. The monitoring methods focus on aberration detection in count data time series from public health surveillance of communicable diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics, or social sciences. The package implements many typical outbreak detection procedures such as the (improved) Farrington algorithm, or the negative binomial GLR-CUSUM method of Hoehle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>. A novel CUSUM approach combining logistic and multinomial logistic modeling is also included. The package contains several real-world data sets, the ability to simulate outbreak data, and to visualize the results of the monitoring in a temporal, spatial or spatio-temporal fashion. A recent overview of the available monitoring procedures is given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>. For the retrospective analysis of epidemic spread, the package provides three endemic-epidemic modeling frameworks with tools for visualization, likelihood inference, and simulation. hhh4() estimates models for (multivariate) count time series following Paul and Held (2011) <doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>. twinSIR() models the susceptible-infectious-recovered (SIR) event history of a fixed population, e.g, epidemics across farms or networks, as a multivariate point process as proposed by Hoehle (2009) <doi:10.1002/bimj.200900050>. twinstim() estimates self-exciting point process models for a spatio-temporal point pattern of infective events, e.g., time-stamped geo-referenced surveillance data, as proposed by Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>. A recent overview of the implemented space-time modeling frameworks for epidemic phenomena is given by Meyer et al. (2017) <doi:10.18637/jss.v077.i11>.

Maintained by Sebastian Meyer. Last updated 6 hours ago.

cpp

2 stars 10.65 score 446 scripts 3 dependents

bioc

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 scripts

bioc

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

geoffjentry

twitteR:R Based Twitter Client

Provides an interface to the Twitter web API.

Maintained by Jeff Gentry. Last updated 9 years ago.

254 stars 10.12 score 2.0k scripts 1 dependents

bioc

matter:Out-of-core statistical computing and signal processing

Toolbox for larger-than-memory scientific computing and visualization, providing efficient out-of-core data structures using files or shared memory, for dense and sparse vectors, matrices, and arrays, with applications to nonuniformly sampled signals and images.

Maintained by Kylie A. Bemis. Last updated 4 months ago.

infrastructuredatarepresentationdataimportdimensionreductionpreprocessingcpp

57 stars 9.52 score 64 scripts 2 dependents

bioc

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-forge

ClassDiscovery:Classes and Methods for "Class Discovery" with Microarrays or Proteomics

Defines the classes used for "class discovery" problems in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance.

Maintained by Kevin R. Coombes. Last updated 2 months ago.

microarrayclustering

8.53 score 85 scripts 9 dependents

swihart

rmutil:Utilities for Nonlinear Regression and Repeated Measurements Models

A toolkit of functions for nonlinear regression and repeated measurements not to be used by itself but called by other Lindsey packages such as 'gnlm', 'stable', 'growth', 'repeated', and 'event' (available at <https://www.commanster.eu/rcode.html>).

Maintained by Bruce Swihart. Last updated 2 years ago.

fortran

1 stars 8.35 score 358 scripts 70 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

bioc

motifStack:Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.

Maintained by Jianhong Ou. Last updated 3 months ago.

sequencematchingvisualizationsequencingmicroarrayalignmentchipchipchipseqmotifannotationdataimport

7.93 score 188 scripts 6 dependents

cran

timeSeries:Financial Time Series Objects (Rmetrics)

'S4' classes and various tools for financial time series: Basic functions such as scaling and sorting, subsetting, mathematical operations and statistical functions.

Maintained by Georgi N. Boshnakov. Last updated 6 months ago.

2 stars 7.89 score 146 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

bnprks

BPCells:Single Cell Counts Matrices to PCA

> Efficient operations for single cell ATAC-seq fragments and RNA counts matrices. Interoperable with standard file formats, and introduces efficient bit-packed formats that allow large storage savings and increased read speeds.

Maintained by Benjamin Parks. Last updated 2 months ago.

zlibhdf5cpp

184 stars 7.48 score 172 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 Pérez - Goya. Last updated 11 months ago.

satellite-images

54 stars 7.45 score 52 scripts

ssnn-airr

shazam:Immunoglobulin Somatic Hypermutation Analysis

Provides a computational framework for analyzing mutations in immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of antigen-driven selection pressure, mutational load quantification, building of somatic hypermutation (SHM) models, and model-dependent distance calculations. Also includes empirically derived models of SHM for both mice and humans. Citations: Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>, Yaari, et al (2012) <doi:10.1093/nar/gks457>, Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>, Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.

Maintained by Susanna Marquez. Last updated 3 months ago.

7.43 score 222 scripts 2 dependents

choi-phd

TestDesign:Optimal Test Design Approach to Fixed and Adaptive Test Construction

Uses the optimal test design approach by Birnbaum (1968, ISBN:9781593119348) and van der Linden (2018) <doi:10.1201/9781315117430> to construct fixed, adaptive, and parallel tests. Supports the following mixed-integer programming (MIP) solver packages: 'Rsymphony', 'highs', 'gurobi', 'lpSolve', and 'Rglpk'. The 'gurobi' package is not available from CRAN; see <https://www.gurobi.com/downloads/>.

Maintained by Seung W. Choi. Last updated 6 months ago.

openblascpp

3 stars 7.34 score 37 scripts 2 dependents

bioc

IHW:Independent Hypothesis Weighting

Independent hypothesis weighting (IHW) is a multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input to IHW is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis.

Maintained by Nikos Ignatiadis. Last updated 5 months ago.

immunooncologymultiplecomparisonrnaseq

7.25 score 264 scripts 2 dependents

jellegoeman

penalized:L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation in GLMs and in the Cox Model

Fitting possibly high dimensional penalized regression models. The penalty structure can be any combination of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity constraint on the regression coefficients. The supported regression models are linear, logistic and Poisson regression and the Cox Proportional Hazards model. Cross-validation routines allow optimization of the tuning parameters.

Maintained by Jelle Goeman. Last updated 3 years ago.

openblascpp

4 stars 7.09 score 429 scripts 17 dependents

bioc

HiCExperiment:Bioconductor class for interacting with Hi-C files in R

R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The `HiCExperiment` class stores the Hi-C contacts parsed from local contact matrix files. `HiCExperiment` instances can be further investigated in R using the `HiContacts` analysis package.

Maintained by Jacques Serizay. Last updated 10 days ago.

hicdna3dstructuredataimport

9 stars 7.02 score 48 scripts 2 dependents

r-forge

oompaBase:Class Unions, Matrix Operations, and Color Schemes for OOMPA

Provides the class unions that must be preloaded in order for the basic tools in the OOMPA (Object-Oriented Microarray and Proteomics Analysis) project to be defined and loaded. It also includes vectorized operations for row-by-row means, variances, and t-tests. Finally, it provides new color schemes. Details on the packages in the OOMPA project can be found at <http://oompa.r-forge.r-project.org/>.

Maintained by Kevin R. Coombes. Last updated 2 months ago.

infrastructure

6.97 score 29 scripts 18 dependents

archaeostat

ArchaeoPhases:Post-Processing of Markov Chain Monte Carlo Simulations for Chronological Modelling

Statistical analysis of archaeological dates and groups of dates. This package allows to post-process Markov Chain Monte Carlo (MCMC) simulations from 'ChronoModel' <https://chronomodel.com/>, 'Oxcal' <https://c14.arch.ox.ac.uk/oxcal.html> or 'BCal' <https://bcal.shef.ac.uk/>. It provides functions for the study of rhythms of the long term from the posterior distribution of a series of dates (tempo and activity plot). It also allows the estimation and visualization of time ranges from the posterior distribution of groups of dates (e.g. duration, transition and hiatus between successive phases) as described in Philippe and Vibet (2020) <doi:10.18637/jss.v093.c01>.

Maintained by Anne Philippe. Last updated 12 months ago.

archaeologybayesian-statisticsgeochronologymarkov-chainradiocarbon-dates

10 stars 6.90 score 66 scripts

calvagone

campsismod:Generic Implementation of a PK/PD Model

A generic, easy-to-use and expandable implementation of a pharmacokinetic (PK) / pharmacodynamic (PD) model based on the S4 class system. This package allows the user to read/write a pharmacometric model from/to files and adapt it further on the fly in the R environment. For this purpose, this package provides an intuitive API to add, modify or delete equations, ordinary differential equations (ODE's), model parameters or compartment properties (like infusion duration or rate, bioavailability and initial values). Finally, this package also provides a useful export of the model for use with simulation packages 'rxode2' and 'mrgsolve'. This package is designed and intended to be used with package 'campsis', a PK/PD simulation platform built on top of 'rxode2' and 'mrgsolve'.

Maintained by Nicolas Luyckx. Last updated 12 days ago.

5 stars 6.82 score 42 scripts 1 dependents

spluque

diveMove:Dive Analysis and Calibration

Utilities to represent, visualize, filter, analyse, and summarize time-depth recorder (TDR) data. Miscellaneous functions for handling location data are also provided.

Maintained by Sebastian P. Luque. Last updated 6 months ago.

animal-behaviorbehavioural-ecologybiologydivingscience

6 stars 6.75 score 55 scripts

toxpi

toxpiR:Create ToxPi Prioritization Models

Enables users to build 'ToxPi' prioritization models and provides functionality within the grid framework for plotting ToxPi graphs. 'toxpiR' allows for more customization than the 'ToxPi GUI' (<https://toxpi.org>) and integration into existing workflows for greater ease-of-use, reproducibility, and transparency. toxpiR package behaves nearly identically to the GUI; the package documentation includes notes about all differences. The vignettes download example files from <https://github.com/ToxPi/ToxPi-example-files>.

Maintained by Jonathon F Fleming. Last updated 7 months ago.

data-sciencemodelingtoxicology

11 stars 6.58 score 19 scripts

r-forge

ClassComparison:Classes and Methods for "Class Comparison" Problems on Microarrays

Defines the classes used for "class comparison" problems in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class comparison includes tests for differential expression; see Simon's book for details on typical problem types.

Maintained by Kevin R. Coombes. Last updated 2 months ago.

microarraydifferentialexpressionmultiplecomparisons

6.46 score 44 scripts 3 dependents

rickhelmus

patRoon:Workflows for Mass-Spectrometry Based Non-Target Analysis

Provides an easy-to-use interface to a mass spectrometry based non-target analysis workflow. Various (open-source) tools are combined which provide algorithms for extraction and grouping of features, extraction of MS and MS/MS data, automatic formula and compound annotation and grouping related features to components. In addition, various tools are provided for e.g. data preparation and cleanup, plotting results and automatic reporting.

Maintained by Rick Helmus. Last updated 7 days ago.

mass-spectrometrynon-targetcppopenjdk

65 stars 6.24 score 43 scripts

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 dependents

bioc

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

dami82

mutSignatures:Decipher Mutational Signatures from Somatic Mutational Catalogs

Cancer cells accumulate DNA mutations as result of DNA damage and DNA repair processes. This computational framework is aimed at deciphering DNA mutational signatures operating in cancer. The framework includes modules that support raw data import and processing, mutational signature extraction, and results interpretation and visualization. The framework accepts widely used file formats storing information about DNA variants, such as Variant Call Format files. The framework performs Non-Negative Matrix Factorization to extract mutational signatures explaining the observed set of DNA mutations. Bootstrapping is performed as part of the analysis. The framework supports parallelization and is optimized for use on multi-core systems. The software was described by Fantini D et al (2020) <doi:10.1038/s41598-020-75062-0> and is based on a custom R-based implementation of the original MATLAB WTSI framework by Alexandrov LB et al (2013) <doi:10.1016/j.celrep.2012.12.008>.

Maintained by Damiano Fantini. Last updated 2 years ago.

14 stars 5.83 score 48 scripts

dpmcsuss

iGraphMatch:Tools for Graph Matching

Versatile tools and data for graph matching analysis with various forms of prior information that supports working with 'igraph' objects, matrix objects, or lists of either.

Maintained by Daniel Sussman. Last updated 11 months ago.

graph-algorithmsgraph-matchingcpp

9 stars 5.65 score 9 scripts

bioc

GenomicTuples:Representation and Manipulation of Genomic Tuples

GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package.

Maintained by Peter Hickey. Last updated 5 months ago.

infrastructuredatarepresentationsequencingcpp

4 stars 5.48 score 7 scripts

ssnn-airr

scoper:Spectral Clustering-Based Method for Identifying B Cell Clones

Provides a computational framework for identification of B cell clones from Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data. Three main functions are included (identicalClones, hierarchicalClones, and spectralClones) that perform clustering among sequences of BCRs/IGs (B cell receptors/immunoglobulins) which share the same V gene, J gene and junction length. Nouri N and Kleinstein SH (2018) <doi: 10.1093/bioinformatics/bty235>. Nouri N and Kleinstein SH (2019) <doi: 10.1101/788620>. Gupta NT, et al. (2017) <doi: 10.4049/jimmunol.1601850>.

Maintained by Susanna Marquez. Last updated 2 months ago.

cpp

5.43 score 89 scripts

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

8 stars 5.35 score 56 scripts

centerforstatistics-ugent

pim:Fit Probabilistic Index Models

Fit a probabilistic index model as described in Thas et al, 2012: <doi:10.1111/j.1467-9868.2011.01020.x>. The interface to the modeling function has changed in this new version. The old version is still available at R-Forge.

Maintained by Joris Meys. Last updated 3 months ago.

modellingstatistics

10 stars 5.33 score 43 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 8 days ago.

cpp

1 stars 5.22 score 1 dependents

jaganmn

flint:Fast Library for Number Theory

An R interface to 'FLINT' <https://flintlib.org/>, a C library for number theory. 'FLINT' extends GNU 'MPFR' <https://www.mpfr.org/> and GNU 'MP' <https://gmplib.org/> with support for operations on standard rings (the integers, the integers modulo n, finite fields, the rational, p-adic, real, and complex numbers) as well as matrices and polynomials over rings. 'FLINT' implements midpoint-radius interval arithmetic, also known as ball arithmetic, in the real and complex numbers, enabling computation in arbitrary precision with rigorous propagation of rounding errors; see Johansson (2017) <doi:10.1109/TC.2017.2690633>. Finally, 'FLINT' provides ball arithmetic implementations of many special mathematical functions, with high coverage of reference works such as the NIST Digital Library of Mathematical Functions <https://dlmf.nist.gov/>. The R interface defines S4 classes, generic functions, and methods for representation and basic operations as well as plain R functions mirroring and vectorizing entry points in the C library.

Maintained by Mikael Jagan. Last updated 4 days ago.

flintmpfr4gmp

5 stars 5.11 score 20 scripts

tesselle

tabula:Analysis and Visualization of Archaeological Count Data

An easy way to examine archaeological count data. This package provides several tests and measures of diversity: heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.), richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and similarity (Brainerd-Robinson, etc.). It allows to easily visualize count data and statistical thresholds: rank vs abundance plots, heatmaps, Ford (1962) and Bertin (1977) diagrams, etc.

Maintained by Nicolas Frerebeau. Last updated 25 days ago.

data-visualizationarchaeologyarchaeological-science

5.10 score 38 scripts 1 dependents

bioc

epivizrData:Data Management API for epiviz interactive visualization app

Serve data from Bioconductor Objects through a WebSocket connection.

Maintained by Hector Corrada Bravo. Last updated 5 months ago.

infrastructurevisualization

1 stars 5.08 score 4 scripts 4 dependents

bioc

PWMEnrich:PWM enrichment analysis

A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.

Maintained by Diego Diez. Last updated 5 months ago.

motifannotationsequencematchingsoftware

5.08 score 60 scripts

bioc

scanMiRApp:scanMiR shiny application

A shiny interface to the scanMiR package. The application enables the scanning of transcripts and custom sequences for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data. In addition contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames, and some utilities for facilitating scans and identifying enriched miRNA-target pairs.

Maintained by Pierre-Luc Germain. Last updated 5 months ago.

mirnasequencematchingguishinyapps

4.76 score 19 scripts

bioc

ChIPseqR:Identifying Protein Binding Sites in High-Throughput Sequencing Data

ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.

Maintained by Peter Humburg. Last updated 5 months ago.

chipseqinfrastructure

4.70 score 1 scripts

tesselle

kairos:Analysis of Chronological Patterns from Archaeological Count Data

A toolkit for absolute and relative dating and analysis of chronological patterns. This package includes functions for chronological modeling and dating of archaeological assemblages from count data. It provides methods for matrix seriation. It also allows to compute time point estimates and density estimates of the occupation and duration of an archaeological site.

Maintained by Nicolas Frerebeau. Last updated 25 days ago.

chronologymatrix-seriationarchaeologyarchaeological-science

4.66 score 11 scripts 1 dependents

guidoamoreira

bayesPO:Bayesian Inference for Presence-Only Data

Presence-Only data is best modelled with a Point Process Model. The work of Moreira and Gamerman (2022) <doi:10.1214/21-AOAS1569> provides a way to use exact Bayesian inference to model this type of data, which is implemented in this package.

Maintained by Guido Alberti Moreira. Last updated 5 months ago.

cppopenmp

3 stars 4.65 score 2 scripts

bioc

BiocHail:basilisk and hail

Use hail via basilisk when appropriate, or via reticulate. This package can be used in terra.bio to interact with UK Biobank resources processed by hail.is.

Maintained by Vincent Carey. Last updated 4 months ago.

infrastructurebioconductorgeneticshail

6 stars 4.53 score 19 scripts

mikemahoney218

mvdf:A Minimum Viable Data Format for 3D Rendering via Blender

A small, self-contained, minimum viable data format providing a standard interface for using R as a front-end for the Blender 3D rendering program. The core approach centers around an S4 class, 'mvdf', with getter, setter, and validation methods designed to be extended for more specific rendering approaches.

Maintained by Michael Mahoney. Last updated 4 years ago.

blender

16 stars 4.20 score 5 scripts

petermeissner

hellno:A Solution to the 'stringsAsFactors=FALSE' Problem

Base R's default setting for 'stringsAsFactors' within 'data.frame()' and 'as.data.frame()' is supposedly the most often complained about piece of code in the R infrastructure. The 'hellno' package provides an explicit solution without changing R itself or having to mess around with options. It tries to solve this problem by providing alternative 'data.frame()' and 'as.data.frame()' functions that are in fact simple wrappers around base R's 'data.frame()', 'as.data.frame()', 'rbind()' and 'rbind.as.data.frame()' with 'stringsAsFactors' option set to 'HELLNO' (which in turn equals FALSE) by default.

Maintained by Peter Meissner. Last updated 7 years ago.

2 stars 4.18 score 8 scripts 5 dependents

bioc

PING:Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data

Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.

Maintained by Renan Sauteraud. Last updated 2 days ago.

clusteringstatisticalmethodvisualizationsequencinggsl

4.18 score 7 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

robinhankin

multivator:A Multivariate Emulator

A multivariate generalization of the emulator package.

Maintained by Robin K. S. Hankin. Last updated 2 years ago.

3.62 score 21 scripts

cnrakt

haplotypes:Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony

Provides S4 classes and methods for reading and manipulating aligned DNA sequences, supporting an indel coding methods (only simple indel coding method is available in the current version), showing base substitutions and indels, calculating absolute pairwise distances between DNA sequences, and collapses identical DNA sequences into haplotypes or inferring haplotypes using user provided absolute pairwise character difference matrix. This package also includes S4 classes and methods for estimating genealogical relationships among haplotypes using statistical parsimony and plotting parsimony networks.

Maintained by Caner Aktas. Last updated 2 years ago.

1 stars 3.43 score 54 scripts

bioc

epigenomix:Epigenetic and gene transcription data normalization and integration with mixture models

A package for the integrative analysis of RNA-seq or microarray based gene transcription and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.

Maintained by Hans-Ulrich Klein. Last updated 5 months ago.

chipseqgeneexpressiondifferentialexpressionclassification

3.30 score 1 scripts

flr

FLFleet:Classes and Methods for Fleets and Metiers

This package contains classes and methods for modelling of fishing fleets and their activity on multiple fish stocks.

Maintained by Iago Mosqueira. Last updated 2 years ago.

1 stars 3.11 score 86 scripts 1 dependents

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.

openjdk

3.06 score 19 scripts

cran

ibmdbR:IBM in-Database Analytics for R

Functionality required to efficiently use R with IBM(R) Db2(R) Warehouse offerings (formerly IBM dashDB(R)) and IBM Db2 for z/OS(R) in conjunction with IBM Db2 Analytics Accelerator for z/OS. Many basic and complex R operations are pushed down into the database, which removes the main memory boundary of R and allows to make full use of parallel processing in the underlying database. For executing R-functions in a multi-node environment in parallel the idaTApply() function requires the 'SparkR' package (<https://spark.apache.org/docs/latest/sparkr.html>). The optional 'ggplot2' package is needed for the plot.idaLm() function only.

Maintained by Shaikh Quader. Last updated 1 years ago.

2 stars 3.00 score

ptaranti

coppeCosenzaR:COPPE-Cosenza Fuzzy Hierarchy Model

The program implements the COPPE-Cosenza Fuzzy Hierarchy Model. The model was based on the evaluation of local alternatives, representing regional potentialities, so as to fulfill demands of economic projects. After defining demand profiles in terms of their technological coefficients, the degree of importance of factors is defined so as to represent the productive activity. The method can detect a surplus of supply without the restriction of the distance of classical algebra, defining a hierarchy of location alternatives. In COPPE-Cosenza Model, the distance between factors is measured in terms of the difference between grades of memberships of the same factors belonging to two or more sets under comparison. The required factors are classified under the following linguistic variables: Critical (CR); Conditioning (C); Little Conditioning (LC); and Irrelevant (I). And the alternatives can assume the following linguistic variables: Excellent (Ex), Good (G), Regular (R), Weak (W), Empty (Em), Zero (Z) and Inexistent (In). The model also provides flexibility, allowing different aggregation rules to be performed and defined by the Decision Maker. Such feature is considered in this package, allowing the user to define other aggregation matrices, since it considers the same linguistic variables mentioned.

Maintained by Pier Taranti. Last updated 5 years ago.

coppe-cosenza

3.00 score 20 scripts

jacobnabe

DEPONS2R:Read, Plot and Analyse Output from the DEPONS Model

Methods for analyzing population dynamics and movement tracks simulated using the DEPONS model <https://www.depons.eu> (v.3.0), for manipulating input raster files, shipping routes and for analyzing sound propagated from ships.

Maintained by Jacob Nabe-Nielsen. Last updated 7 hours ago.

agent-based-modelingenvironmental-modellingmarine-biology

2.90 score 4 scripts

oscarperpinan

solaR:Radiation and Photovoltaic Systems

Calculation methods of solar radiation and performance of photovoltaic systems from daily and intradaily irradiation data sources.

Maintained by Oscar Perpiñán Lamigueiro. Last updated 3 years ago.

1 stars 2.74 score 55 scripts

guidoamoreira

pompp:Presence-Only for Marked Point Process

Inspired by Moreira and Gamerman (2022) <doi:10.1214/21-AOAS1569>, this methodology expands the idea by including Marks in the point process. Using efficient 'C++' code, the estimation is possible and made faster with 'OpenMP' <https://www.openmp.org/> enabled computers. This package was developed under the project PTDC/MAT-STA/28243/2017, supported by Portuguese funds through the Portuguese Foundation for Science and Technology (FCT).

Maintained by Guido Alberti Moreira. Last updated 2 years ago.

cppopenmp

2.70 score

ablommaert

spectralAnalysis:Pre-Process, Visualize and Analyse Spectral Data

Infrared, near-infrared and Raman spectroscopic data measured during chemical reactions, provide structural fingerprints by which molecules can be identified and quantified. The application of these spectroscopic techniques as inline process analytical tools (PAT), provides the pharmaceutical and chemical industry with novel tools, allowing to monitor their chemical processes, resulting in a better process understanding through insight in reaction rates, mechanistics, stability, etc. Data can be read into R via the generic spc-format, which is generally supported by spectrometer vendor software. Versatile pre-processing functions are available to perform baseline correction by linking to the 'baseline' package; noise reduction via the 'signal' package; as well as time alignment, normalization, differentiation, integration and interpolation. Implementation based on the S4 object system allows storing a pre-processing pipeline as part of a spectral data object, and easily transferring it to other datasets. Interactive plotting tools are provided based on the 'plotly' package. Non-negative matrix factorization (NMF) has been implemented to perform multivariate analyses on individual spectral datasets or on multiple datasets at once. NMF provides a parts-based representation of the spectral data in terms of spectral signatures of the chemical compounds and their relative proportions. See 'hNMF'-package for references on available methods. The functionality to read in spc-files was adapted from the 'hyperSpec' package.

Maintained by Adriaan Blommaert. Last updated 1 years ago.

2.26 score 18 scripts

ethanbass

entab:Entab

Entab is a record-format file reader.

Maintained by Roderick. Last updated 3 years ago.

rustcargo

1 stars 2.00 score 2 scripts

cran

GenAlgo:Classes and Methods to Use Genetic Algorithms for Feature Selection

Defines classes and methods that can be used to implement genetic algorithms for feature selection. The idea is that we want to select a fixed number of features to combine into a linear classifier that can predict a binary outcome, and can use a genetic algorithm heuristically to select an optimal set of features.

Maintained by Kevin R. Coombes. Last updated 4 years ago.

microarrayclustering

2.00 score

cran

epxToR:Import 'Epidata' XML Files '.epx'

Import data from 'Epidata' XML files '.epx' and convert it to R data structures.

Maintained by Jean Pierre Decorps. Last updated 5 years ago.

1.70 score

cran

eDMA:Dynamic Model Averaging with Grid Search

Perform dynamic model averaging with grid search as in Dangl and Halling (2012) <doi:10.1016/j.jfineco.2012.04.003> using parallel computing.

Maintained by Leopoldo Catania. Last updated 7 years ago.

openblascppopenmp

1.70 score

: