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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

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

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

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

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 dependents

bioc

microbiome:Microbiome Analytics

Utilities for microbiome analysis.

Maintained by Leo Lahti. Last updated 5 months ago.

metagenomicsmicrobiomesequencingsystemsbiologyhitchiphitchip-atlashuman-microbiomemicrobiologymicrobiome-analysisphyloseqpopulation-study

293 stars 12.51 score 2.0k scripts 5 dependents

stuart-lab

Signac:Analysis of Single-Cell Chromatin Data

A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.

Maintained by Tim Stuart. Last updated 7 months ago.

atacbioinformaticssingle-cellzlibcpp

355 stars 12.18 score 3.7k scripts 1 dependents

bioc

ShortRead:FASTQ input and manipulation

This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

dataimportsequencingqualitycontrolbioconductor-packagecore-packagezlibcpp

8 stars 12.08 score 1.8k scripts 49 dependents

emf-creaf

indicspecies:Relationship Between Species and Groups of Sites

Functions to assess the strength and statistical significance of the relationship between species occurrence/abundance and groups of sites [De Caceres & Legendre (2009) <doi:10.1890/08-1823.1>]. Also includes functions to measure species niche breadth using resource categories [De Caceres et al. (2011) <doi:10.1111/J.1600-0706.2011.19679.x>].

Maintained by Miquel De Cáceres. Last updated 1 months ago.

10 stars 9.66 score 386 scripts 4 dependents

vigou3

actuar:Actuarial Functions and Heavy Tailed Distributions

Functions and data sets for actuarial science: modeling of loss distributions; risk theory and ruin theory; simulation of compound models, discrete mixtures and compound hierarchical models; credibility theory. Support for many additional probability distributions to model insurance loss size and frequency: 23 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete distribution; zero-truncated and zero-modified extensions of the standard discrete distributions. Support for phase-type distributions commonly used to compute ruin probabilities. Main reference: <doi:10.18637/jss.v025.i07>. Implementation of the Feller-Pareto family of distributions: <doi:10.18637/jss.v103.i06>.

Maintained by Vincent Goulet. Last updated 3 months ago.

openblas

12 stars 9.44 score 732 scripts 35 dependents

ohdsi

Cyclops:Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis

This model fitting tool incorporates cyclic coordinate descent and majorization-minimization approaches to fit a variety of regression models found in large-scale observational healthcare data. Implementations focus on computational optimization and fine-scale parallelization to yield efficient inference in massive datasets. Please see: Suchard, Simpson, Zorych, Ryan and Madigan (2013) <doi:10.1145/2414416.2414791>.

Maintained by Marc A. Suchard. Last updated 4 months ago.

hadescpp

39 stars 9.05 score 73 scripts 4 dependents

bioc

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 10 days ago.

alignmentsequencematchingsequencinggeneticsbioconductor-package

1 stars 8.48 score 27 scripts 104 dependents

ropensci

ritis:Integrated Taxonomic Information System Client

An interface to the Integrated Taxonomic Information System ('ITIS') (<https://www.itis.gov>). Includes functions to work with the 'ITIS' REST API methods (<https://www.itis.gov/ws_description.html>), as well as the 'Solr' web service (<https://www.itis.gov/solr_documentation.html>).

Maintained by Julia Blum. Last updated 2 months ago.

taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperitistaxize

16 stars 7.72 score 64 scripts 24 dependents

projectmosaic

mosaicCore:Common Utilities for Other MOSAIC-Family Packages

Common utilities used in other MOSAIC-family packages are collected here.

Maintained by Randall Pruim. Last updated 1 years ago.

1 stars 7.07 score 113 scripts 26 dependents

fcharte

mldr:Exploratory Data Analysis and Manipulation of Multi-Label Data Sets

Exploratory data analysis and manipulation functions for multi- label data sets along with an interactive Shiny application to ease their use.

Maintained by David Charte. Last updated 5 years ago.

23 stars 7.07 score 168 scripts 2 dependents

bioc

GenomicFiles:Distributed computing by file or by range

This package provides infrastructure for parallel computations distributed 'by file' or 'by range'. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

geneticsinfrastructuredataimportsequencingcoverage

6.86 score 89 scripts 16 dependents

chelbert

DiceDesign:Designs of Computer Experiments

Space-Filling Designs and space-filling criteria (distance-based and uniformity-based), with emphasis to computer experiments; <doi:10.18637/jss.v065.i11>.

Maintained by Celine Helbert. Last updated 1 years ago.

6.12 score 231 scripts 64 dependents

bioc

HiContacts:Analysing cool files in R with HiContacts

HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.

Maintained by Jacques Serizay. Last updated 10 days ago.

hicdna3dstructure

12 stars 6.07 score 49 scripts

njtierney

maxcovr:A Set of Tools For Solving The Maximal Covering Location Problem

Solving the "maximal covering location problem" as described by Church can be difficult for users not familiar with linear programming. maxcovr provides functions to make it easy to solve this problem, and tools to calculate facility coverage.

Maintained by Nicholas Tierney. Last updated 4 months ago.

distancelinear-programmingcpp

43 stars 6.05 score 43 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

emilio-berti

GHCNr:Download Weather Station Data from GHCNd

The goal of 'GHCNr' is to provide a fast and friendly interface with the Global Historical Climatology Network daily (GHCNd) database, which contains daily summaries of weather station data worldwide (<https://www.ncei.noaa.gov/products/land-based-station/global-historical-climatology-network-daily>). GHCNd is accessed through the web API <https://www.ncei.noaa.gov/access/services/data/v1>. 'GHCNr' main functionalities consist of downloading data from GHCNd, filter it, and to aggregate it at monthly and annual scales.

Maintained by Emilio Berti. Last updated 3 months ago.

2 stars 4.95 score 3 scripts

martirm

clustAnalytics:Cluster Evaluation on Graphs

Evaluates the stability and significance of clusters on 'igraph' graphs. Supports weighted and unweighted graphs. Implements the cluster evaluation methods defined by Arratia A, Renedo M (2021) <doi:10.7717/peerj-cs.600>. Also includes an implementation of the Reduced Mutual Information introduced by Newman et al. (2020) <doi:10.1103/PhysRevE.101.042304>.

Maintained by Martí Renedo Mirambell. Last updated 1 years ago.

cpp

5 stars 4.92 score 33 scripts

ericmarcon

divent:Entropy Partitioning to Measure Diversity

Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>. 'divent' provides functions to estimate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity.

Maintained by Eric Marcon. Last updated 1 months ago.

cpp

1 stars 4.78 score 1 scripts

bioc

scmeth:Functions to conduct quality control analysis in methylation data

Functions to analyze methylation data can be found here. Some functions are relevant for single cell methylation data but most other functions can be used for any methylation data. Highlight of this workflow is the comprehensive quality control report.

Maintained by Divy Kangeyan. Last updated 5 months ago.

dnamethylationqualitycontrolpreprocessingsinglecellimmunooncologybioconductor-packagemethylationsingle-cell-methylation

4.70 score 5 scripts

koenniem

mpathsenser:Process and Analyse Data from m-Path Sense

Overcomes one of the major challenges in mobile (passive) sensing, namely being able to pre-process the raw data that comes from a mobile sensing app, specifically 'm-Path Sense' <https://m-path.io>. The main task of 'mpathsenser' is therefore to read 'm-Path Sense' JSON files into a database and provide several convenience functions to aid in data processing.

Maintained by Koen Niemeijer. Last updated 1 months ago.

mobile-sensing

1 stars 4.30 score 6 scripts

cenwu

pqrBayes:Bayesian Penalized Quantile Regression

Bayesian regularized quantile regression utilizing sparse priors to impose exact sparsity leads to efficient Bayesian shrinkage estimation, variable selection and statistical inference. In this package, we have implemented robust Bayesian variable selection with spike-and-slab priors under high-dimensional linear regression models (Fan et al. (2024) <doi:10.3390/e26090794> and Ren et al. (2023) <doi:10.1111/biom.13670>), and regularized quantile varying coefficient models (Zhou et al.(2023) <doi:10.1016/j.csda.2023.107808>). In particular, valid robust Bayesian inferences under both models in the presence of heavy-tailed errors can be validated on finite samples. The Markov Chain Monte Carlo (MCMC) algorithms of the proposed and alternative models are implemented in C++.

Maintained by Cen Wu. Last updated 1 months ago.

openblascppopenmp

3 stars 3.95 score

cran

BAT:Biodiversity Assessment Tools

Includes algorithms to assess alpha and beta diversity in all their dimensions (taxonomic, phylogenetic and functional). It allows performing a number of analyses based on species identities/abundances, phylogenetic/functional distances, trees, convex-hulls or kernel density n-dimensional hypervolumes depicting species relationships. Cardoso et al. (2015) <doi:10.1111/2041-210X.12310>.

Maintained by Pedro Cardoso. Last updated 1 years ago.

3.17 score 3 dependents

jeinbeck-code

LPCM:Local Principal Curve Methods

Fitting multivariate data patterns with local principal curves, including tools for data compression (projection) and measuring goodness-of-fit; with some additional functions for mean shift clustering. See Einbeck, Tutz and Evers (2005) <doi:10.1007/s11222-005-4073-8> and Ameijeiras-Alonso and Einbeck (2023) <doi:10.1007/s11634-023-00575-1>.

Maintained by Jochen Einbeck. Last updated 7 months ago.

3.09 score 35 scripts 1 dependents

jyklly

Rgbp:Hierarchical Modeling and Frequency Method Checking on Overdispersed Gaussian, Poisson, and Binomial Data

We utilize approximate Bayesian machinery to fit two-level conjugate hierarchical models on overdispersed Gaussian, Poisson, and Binomial data and evaluates whether the resulting approximate Bayesian interval estimates for random effects meet the nominal confidence levels via frequency coverage evaluation. The data that Rgbp assumes comprise observed sufficient statistic for each random effect, such as an average or a proportion of each group, without population-level data. The approximate Bayesian tool equipped with the adjustment for density maximization produces approximate point and interval estimates for model parameters including second-level variance component, regression coefficients, and random effect. For the Binomial data, the package provides an option to produce posterior samples of all the model parameters via the acceptance-rejection method. The package provides a quick way to evaluate coverage rates of the resultant Bayesian interval estimates for random effects via a parametric bootstrapping, which we call frequency method checking.

Maintained by Joseph Kelly. Last updated 7 years ago.

3 stars 2.95 score 15 scripts

rwparsons

simMetric:Metrics (with Uncertainty) for Simulation Studies that Evaluate Statistical Methods

Allows users to quickly apply individual or multiple metrics to evaluate Monte Carlo simulation studies.

Maintained by Rex Parsons. Last updated 2 years ago.

2.70 score 2 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 score

mhoehle

binomSamSize:Confidence Intervals and Sample Size Determination for a Binomial Proportion under Simple Random Sampling and Pooled Sampling

A suite of functions to compute confidence intervals and necessary sample sizes for the parameter p of the Bernoulli B(p) distribution under simple random sampling or under pooled sampling. Such computations are e.g. of interest when investigating the incidence or prevalence in populations. The package contains functions to compute coverage probabilities and coverage coefficients of the provided confidence intervals procedures. Sample size calculations are based on expected length.

Maintained by Michael Hoehle. Last updated 1 years ago.

fortran

2 stars 2.18 score 15 scripts

andrea-fasulo

SAEval:Small Area Estimation Evaluation

Allows users to produce diagnostic procedures and graphic tools for the evaluation of Small Area estimators.

Maintained by Andrea Fasulo. Last updated 2 years ago.

1.00 score

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