Showing 61 of total 61 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
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 10 hours ago.
geospatialrasterspatialvectoronetbbprojgdalgeoscpp
560 stars 17.65 score 17k scripts 856 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 This package has been superseded by the "terra" package 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 2 days ago.
163 stars 17.23 score 58k scripts 562 dependents
r-forge
Matrix:Sparse and Dense Matrix Classes and Methods
A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.
Maintained by Martin Maechler. Last updated 20 days ago.
1 stars 17.23 score 33k scripts 12k dependentsbioc
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 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 Hervé Pagès. Last updated 2 months ago.
infrastructuredatarepresentationbioconductor-packagecore-package
18 stars 16.05 score 1.0k scripts 1.9k dependentsbioc
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
thibautjombart
adegenet:Exploratory Analysis of Genetic and Genomic Data
Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.
Maintained by Zhian N. Kamvar. Last updated 2 months ago.
182 stars 12.60 score 1.9k scripts 29 dependentsbioc
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 17 days ago.
motifannotationgeneregulationmotifdiscoverytranscriptionalignment
28 stars 12.36 score 1.1k scripts 18 dependents
asardaes
dtwclust:Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance
Time series clustering along with optimized techniques related to the Dynamic Time Warping distance and its corresponding lower bounds. Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole clustering are available. Functionality can be easily extended with custom distance measures and centroid definitions. Implementations of DTW barycenter averaging, a distance based on global alignment kernels, and the soft-DTW distance and centroid routines are also provided. All included distance functions have custom loops optimized for the calculation of cross-distance matrices, including parallelization support. Several cluster validity indices are included.
Maintained by Alexis Sarda. Last updated 8 months ago.
clusteringdtwtime-seriesopenblascpp
262 stars 12.35 score 406 scripts 14 dependents
kaneplusplus
bigmemory:Manage Massive Matrices with Shared Memory and Memory-Mapped Files
Create, store, access, and manipulate massive matrices. Matrices are allocated to shared memory and may use memory-mapped files. Packages 'biganalytics', 'bigtabulate', 'synchronicity', and 'bigalgebra' provide advanced functionality.
Maintained by Michael J. Kane. Last updated 1 years ago.
127 stars 11.87 score 920 scripts 64 dependentsbioc
variancePartition:Quantify and interpret drivers of variation in multilevel gene expression experiments
Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. Includes dream differential expression analysis for repeated measures.
Maintained by Gabriel E. Hoffman. Last updated 3 months ago.
rnaseqgeneexpressiongenesetenrichmentdifferentialexpressionbatcheffectqualitycontrolregressionepigeneticsfunctionalgenomicstranscriptomicsnormalizationpreprocessingmicroarrayimmunooncologysoftware
7 stars 11.69 score 1.1k scripts 3 dependents
rudjer
SparseM:Sparse Linear Algebra
Some basic linear algebra functionality for sparse matrices is provided: including Cholesky decomposition and backsolving as well as standard R subsetting and Kronecker products.
Maintained by Roger Koenker. Last updated 9 months ago.
3 stars 11.47 score 306 scripts 1.5k dependentsbioc
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
sgibb
MALDIquant:Quantitative Analysis of Mass Spectrometry Data
A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.
Maintained by Sebastian Gibb. Last updated 7 months ago.
maldimaldi-imsmaldi-tof-msmass-spectrometry
62 stars 11.06 score 180 scripts 44 dependentsbioc
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 10 days ago.
138 stars 10.90 score 1.2k scripts 3 dependentsbioc
ChemmineR:Cheminformatics Toolkit for R
ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.
Maintained by Thomas Girke. Last updated 5 months ago.
cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicscpp
15 stars 10.45 score 253 scripts 12 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 scripts
cran
proxy:Distance and Similarity Measures
Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.
Maintained by David Meyer. Last updated 3 years ago.
3 stars 9.94 score 2.1k dependentsbioc
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
edzer
intervals:Tools for Working with Points and Intervals
Tools for working with and comparing sets of points and intervals.
Maintained by Edzer Pebesma. Last updated 7 months ago.
11 stars 9.50 score 122 scripts 98 dependents
reinhardfurrer
spam:SPArse Matrix
Set of functions for sparse matrix algebra. Differences with other sparse matrix packages are: (1) we only support (essentially) one sparse matrix format, (2) based on transparent and simple structure(s), (3) tailored for MCMC calculations within G(M)RF. (4) and it is fast and scalable (with the extension package spam64). Documentation about 'spam' is provided by vignettes included in this package, see also Furrer and Sain (2010) <doi:10.18637/jss.v036.i10>; see 'citation("spam")' for details.
Maintained by Reinhard Furrer. Last updated 2 months ago.
1 stars 9.36 score 420 scripts 439 dependents
quanteda
quanteda.textstats:Textual Statistics for the Quantitative Analysis of Textual Data
Textual statistics functions formerly in the 'quanteda' package. Textual statistics for characterizing and comparing textual data. Includes functions for measuring term and document frequency, the co-occurrence of words, similarity and distance between features and documents, feature entropy, keyword occurrence, readability, and lexical diversity. These functions extend the 'quanteda' package and are specially designed for sparse textual data.
Maintained by Kenneth Benoit. Last updated 7 months ago.
15 stars 8.91 score 916 scripts 10 dependents
asl
svd:Interfaces to Various State-of-Art SVD and Eigensolvers
R bindings to SVD and eigensolvers (PROPACK, nuTRLan).
Maintained by Anton Korobeynikov. Last updated 3 months ago.
27 stars 8.80 score 244 scripts 30 dependents
alexiosg
rmgarch:Multivariate GARCH Models
Feasible multivariate GARCH models including DCC, GO-GARCH and Copula-GARCH.
Maintained by Alexios Galanos. Last updated 3 months ago.
14 stars 8.51 score 294 scripts 2 dependentsbioc
pwalign:Perform pairwise sequence alignments
The two main functions in the package are pairwiseAlignment() and stringDist(). The former solves (Needleman-Wunsch) global alignment, (Smith-Waterman) local alignment, and (ends-free) overlap alignment problems. The latter computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.
Maintained by Hervé Pagès. Last updated 11 days ago.
alignmentsequencematchingsequencinggeneticsbioconductor-package
1 stars 8.48 score 27 scripts 104 dependents
andreyshabalin
MatrixEQTL:Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations
Matrix eQTL is designed for fast eQTL analysis on large datasets. Matrix eQTL can test for association between genotype and gene expression using linear regression with either additive or ANOVA genotype effects. The models can include covariates to account for factors as population stratification, gender, and clinical variables. It also supports models with heteroscedastic and/or correlated errors, false discovery rate estimation and separate treatment of local (cis) and distant (trans) eQTLs. For more details see Shabalin (2012) <doi:10.1093/bioinformatics/bts163>.
Maintained by Andrey A Shabalin. Last updated 2 years ago.
74 stars 8.31 score 612 scripts 3 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 scriptscran
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
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.
184 stars 7.48 score 172 scripts
trevorhastie
softImpute:Matrix Completion via Iterative Soft-Thresholded SVD
Iterative methods for matrix completion that use nuclear-norm regularization. There are two main approaches.The one approach uses iterative soft-thresholded svds to impute the missing values. The second approach uses alternating least squares. Both have an 'EM' flavor, in that at each iteration the matrix is completed with the current estimate. For large matrices there is a special sparse-matrix class named "Incomplete" that efficiently handles all computations. The package includes procedures for centering and scaling rows, columns or both, and for computing low-rank SVDs on large sparse centered matrices (i.e. principal components).
Maintained by Trevor Hastie. Last updated 4 years ago.
10 stars 7.47 score 253 scripts 22 dependents
robinhankin
onion:Octonions and Quaternions
Quaternions and Octonions are four- and eight- dimensional extensions of the complex numbers. They are normed division algebras over the real numbers and find applications in spatial rotations (quaternions), and string theory and relativity (octonions). The quaternions are noncommutative and the octonions nonassociative. See the package vignette for more details.
Maintained by Robin K. S. Hankin. Last updated 1 months ago.
6 stars 7.27 score 43 scripts 3 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.
4 stars 7.09 score 429 scripts 17 dependentsbioc
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 11 days ago.
9 stars 7.02 score 48 scripts 2 dependents
sritchie73
NetRep:Permutation Testing Network Module Preservation Across Datasets
Functions for assessing the replication/preservation of a network module's topology across datasets through permutation testing; Ritchie et al. (2015) <doi: 10.1016/j.cels.2016.06.012>.
Maintained by Scott Ritchie. Last updated 4 years ago.
12 stars 6.84 score 16 scripts 3 dependents
shabbychef
madness:Automatic Differentiation of Multivariate Operations
An object that supports automatic differentiation of matrix- and multidimensional-valued functions with respect to multidimensional independent variables. Automatic differentiation is via 'forward accumulation'.
Maintained by Steven E. Pav. Last updated 4 years ago.
31 stars 6.59 score 28 scripts 3 dependentsandreyshabalin
filematrix:File-Backed Matrix Class with Convenient Read and Write Access
Interface for working with large matrices stored in files, not in computer memory. Supports multiple non-character data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4 byte real values). Access to parts of the matrix is done by indexing, exactly as with usual R matrices. Supports very large matrices. Tested on multi-terabyte matrices. Allows for more than 2^32 rows or columns. Allows for quick addition of extra columns to a filematrix. Cross-platform as the package has R code only.
Maintained by Andrey A Shabalin. Last updated 6 years ago.
8 stars 6.51 score 45 scripts 2 dependentsbioc
hopach:Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering).
Maintained by Katherine S. Pollard. Last updated 5 months ago.
6.05 score 54 scripts 5 dependentscran
gaston:Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models
Manipulation of genetic data (SNPs). Computation of GRM and dominance matrix, LD, heritability with efficient algorithms for linear mixed model (AIREML). Dandine et al <doi:10.1159/000488519>.
Maintained by Hervé Perdry. Last updated 1 years ago.
5 stars 6.02 score 12 dependents
bbuchsbaum
neuroim:Data Structures and Handling for Neuroimaging Data
A collection of data structures that represent volumetric brain imaging data. The focus is on basic data handling for 3D and 4D neuroimaging data. In addition, there are function to read and write NIFTI files and limited support for reading AFNI files.
Maintained by Bradley Buchsbaum. Last updated 4 years ago.
6 stars 5.64 score 48 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.
10 stars 5.33 score 43 scripts
zzawadz
DepthProc:Statistical Depth Functions for Multivariate Analysis
Data depth concept offers a variety of powerful and user friendly tools for robust exploration and inference for multivariate data. The offered techniques may be successfully used in cases of lack of our knowledge on parametric models generating data due to their nature. The package consist of among others implementations of several data depth techniques involving multivariate quantile-quantile plots, multivariate scatter estimators, multivariate Wilcoxon tests and robust regressions.
Maintained by Zygmunt Zawadzki. Last updated 3 years ago.
depth-functionsexploratory-data-analysisstatisticsopenblascppopenmp
6 stars 5.27 score 104 scripts 2 dependentsbioc
CytoMDS:Low Dimensions projection of cytometry samples
This package implements a low dimensional visualization of a set of cytometry samples, in order to visually assess the 'distances' between them. This, in turn, can greatly help the user to identify quality issues like batch effects or outlier samples, and/or check the presence of potential sample clusters that might align with the exeprimental design. The CytoMDS algorithm combines, on the one hand, the concept of Earth Mover's Distance (EMD), a.k.a. Wasserstein metric and, on the other hand, the Multi Dimensional Scaling (MDS) algorithm for the low dimensional projection. Also, the package provides some diagnostic tools for both checking the quality of the MDS projection, as well as tools to help with the interpretation of the axes of the projection.
Maintained by Philippe Hauchamps. Last updated 2 months ago.
flowcytometryqualitycontroldimensionreductionmultidimensionalscalingsoftwarevisualization
1 stars 5.23 score 2 scripts
bioc
BufferedMatrix:A matrix data storage object held in temporary files
A tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data.
Maintained by Ben Bolstad. Last updated 4 months ago.
4.73 score 6 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.
3 stars 4.65 score 2 scripts
ngmarchant
comparator:Comparison Functions for Clustering and Record Linkage
Implements functions for comparing strings, sequences and numeric vectors for clustering and record linkage applications. Supported comparison functions include: generalized edit distances for comparing sequences/strings, Monge-Elkan similarity for fuzzy comparison of token sets, and L-p distances for comparing numeric vectors. Where possible, comparison functions are implemented in C/C++ to ensure good performance.
Maintained by Neil Marchant. Last updated 3 years ago.
clusteringdistance-measuresdistance-metricsentity-resolutionrecord-linkagesimilarity-measuresstring-similaritycpp
18 stars 4.63 score 47 scriptsrobinhankin
jordan:A Suite of Routines for Working with Jordan Algebras
A Jordan algebra is an algebraic object originally designed to study observables in quantum mechanics. Jordan algebras are commutative but non-associative; they satisfy the Jordan identity. The package follows the ideas and notation of K. McCrimmon (2004, ISBN:0-387-95447-3) "A Taste of Jordan Algebras". To cite the package in publications, please use Hankin (2023) <doi:10.48550/arXiv.2303.06062>.
Maintained by Robin K. S. Hankin. Last updated 9 months ago.
4.60 score 2 scripts
brechtdv
prevalence:Tools for Prevalence Assessment Studies
The prevalence package provides Frequentist and Bayesian methods for prevalence assessment studies. IMPORTANT: the truePrev functions in the prevalence package call on JAGS (Just Another Gibbs Sampler), which therefore has to be available on the user's system. JAGS can be downloaded from <https://mcmc-jags.sourceforge.io/>.
Maintained by Brecht Devleesschauwer. Last updated 3 years ago.
2 stars 4.48 score 38 scripts
yunuuuu
BPCellsArray:Using BPCells as a DelayedArray Backend
Implements a DelayedArray backend for reading and writing arrays in the BPCells storage layout. The resulting BPCells*Arrays are compatible with all Bioconductor pipelines that can accept DelayedArray instances.
Maintained by Yun Peng. Last updated 8 months ago.
softwaredataimportdatarepresentationinfrastructuresingle-cell
7 stars 4.32 score
ggobi
plumbr:Mutable and dynamic data models
The base R data.frame, like any vector, is copied upon modification. This behavior is at odds with that of GUIs and interactive graphics. To rectify this, plumbr provides a mutable, dynamic tabular data model. Models may be chained together to form the complex plumbing necessary for sophisticated graphical interfaces. Also included is a general framework for linking datasets; an typical use case would be a linked brush.
Maintained by Michael Lawrence. Last updated 11 years ago.
18 stars 4.19 score 29 scriptsbioc
unifiedWMWqPCR:Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.
Maintained by Joris Meys. Last updated 5 months ago.
differentialexpressiongeneexpressionmicrotitreplateassaymultiplecomparisonqualitycontrolsoftwarevisualizationqpcr
4.18 score
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 scriptsguidoamoreira
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.
2.70 scorecran
salad:Simple Automatic Differentiation
Handles both vector and matrices, using a flexible S4 class for automatic differentiation. The method used is forward automatic differentiation. Many functions and methods have been defined, so that in most cases, functions written without automatic differentiation in mind can be used without change.
Maintained by Hervé Perdry. Last updated 3 months ago.
2.48 scorecran
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.
2.00 score
hsonne
pathlist:Package Supporting the Work with File Paths
This package implements a S4 class pathlist that internally stores a vector of file paths (as, e.g. received with dir()) as a matrix of path segments. I found out that this is the most compact form to store the paths. The main feature of the class is the dollar function that allows to filter paths for the value of their top-level folder. Using the dollar operator subsequently you can easily narrow down the list of paths. The class implements functions length(), head(), tail(), summary(), and show().
Maintained by Hauke Sonnenberg. Last updated 6 years ago.
1.78 score 2 scripts 2 dependents