R-universe search: exports:start

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.

sequencematching alignment sequencing genetics dataimport datarepresentation infrastructure bioconductor-package core-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.

genetics infrastructure datarepresentation sequencing annotation genomeannotation coverage bioconductor-package core-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.

genetics infrastructure sequencing annotation coverage genomeannotation bioconductor-package core-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.

infrastructure datarepresentation bioconductor-package core-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.

infrastructure datarepresentation bioconductor-package core-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.

infrastructure datarepresentation annotation genomeannotation bioconductor-package core-package u24ca289073

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.

infrastructure dataimport genetics sequencing rnaseq snp coverage alignment immunooncology bioconductor-package core-package

10 stars 15.21 score 3.1k scripts 528 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.

infrastructure bioconductor-package core-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.

genetics infrastructure datarepresentation sequencematching annotation snp bioconductor-package core-package

9 stars 14.12 score 1.2k scripts 267 dependents

bioc

Gviz:Plotting data and annotation information along genomic coordinates

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.

Maintained by Robert Ivanek. Last updated 5 months ago.

visualization microarray sequencing

79 stars 13.08 score 1.4k scripts 48 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.

annotation visualization dataimport zlib openssl curl

12.66 score 6.7k scripts 480 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.

motifannotation generegulation motifdiscovery transcription alignment

28 stars 12.36 score 1.1k scripts 18 dependents

bioc

bsseq:Analyze, manage and store whole-genome methylation data

A collection of tools for analyzing and visualizing whole-genome methylation data from sequencing. This includes whole-genome bisulfite sequencing and Oxford nanopore data.

Maintained by Kasper Daniel Hansen. Last updated 3 months ago.

dnamethylation cpp

37 stars 12.26 score 676 scripts 15 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.

infrastructure datarepresentation bioconductor-package core-package

5 stars 10.99 score 8 scripts 1.2k 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 8 days ago.

cpp

2 stars 10.67 score 446 scripts 3 dependents

predictiveecology

SpaDES.core:Core Utilities for Developing and Running Spatially Explicit Discrete Event Models

Provides the core framework for a discrete event system to implement a complete data-to-decisions, reproducible workflow. The core components facilitate the development of modular pieces, and enable the user to include additional functionality by running user-built modules. Includes conditional scheduling, restart after interruption, packaging of reusable modules, tools for developing arbitrary automated workflows, automated interweaving of modules of different temporal resolution, and tools for visualizing and understanding the within-project dependencies. The suggested package 'NLMR' can be installed from the repository (<https://PredictiveEcology.r-universe.dev>).

Maintained by Eliot J B McIntire. Last updated 1 months ago.

discrete-events-simulations simulation-framework simulation-modeling

10 stars 10.61 score 142 scripts 6 dependents

bioc

GenomicInteractions:Utilities for handling genomic interaction data

Utilities for handling genomic interaction data such as ChIA-PET or Hi-C, annotating genomic features with interaction information, and producing plots and summary statistics.

Maintained by Liz Ing-Simmons. Last updated 5 months ago.

software infrastructure dataimport datarepresentation hic

7 stars 9.31 score 162 scripts 5 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.

alignment sequencematching sequencing genetics bioconductor-package

1 stars 8.48 score 27 scripts 104 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

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.

archaeology bayesian-statistics geochronology markov-chain radiocarbon-dates

10 stars 6.90 score 66 scripts

bioc

VanillaICE:A Hidden Markov Model for high throughput genotyping arrays

Hidden Markov Models for characterizing chromosomal alteration in high throughput SNP arrays.

Maintained by Robert Scharpf. Last updated 5 months ago.

copynumbervariation

5.36 score 63 scripts 1 dependents

r-forge

RobAStBase:Robust Asymptotic Statistics

Base S4-classes and functions for robust asymptotic statistics.

Maintained by Matthias Kohl. Last updated 2 months ago.

4.96 score 64 scripts 4 dependents

datacloning

dcmle:Hierarchical Models Made Easy with Data Cloning

S4 classes around infrastructure provided by the 'coda' and 'dclone' packages to make package development easy as a breeze with data cloning for hierarchical models.

Maintained by Peter Solymos. Last updated 6 months ago.

jags cpp

4.60 score 66 scripts 2 dependents

bioc

ACME:Algorithms for Calculating Microarray Enrichment (ACME)

ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.

Maintained by Sean Davis. Last updated 5 months ago.

technology microarray normalization

4.30 score 4 scripts

bioc

GenomAutomorphism:Compute the automorphisms between DNA's Abelian group representations

This is a R package to compute the automorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group. In a general scenario, from genomic regions till the whole genomes from a given population (from any species or close related species) can be algebraically represented as a direct sum of cyclic groups or more specifically Abelian p-groups. Basically, we propose the representation of multiple sequence alignments of length N bp as element of a finite Abelian group created by the direct sum of homocyclic Abelian group of prime-power order.

Maintained by Robersy Sanchez. Last updated 3 months ago.

mathematicalbiology comparativegenomics functionalgenomics multiplesequencealignment wholegenome genetic-code genetic-code-algebra genome genome-algebra

4.30 score 9 scripts

spkaluzny

splusTimeSeries:Time Series from 'S-PLUS'

A collection of classes and methods for working with indexed rectangular data. The index values can be calendar (timeSeries class) or numeric (signalSeries class). Methods are included for aggregation, alignment, merging, and summaries. The code was originally available in 'S-PLUS'.

Maintained by Stephen Kaluzny. Last updated 6 months ago.

data-structures time-series

3.95 score 20 scripts 1 dependents

dgkf

parttime:Partial Datetime Handling

Datetimes and timestamps are invariably an imprecise notation, with any partial representation implying some amount of uncertainty. To handle this, 'parttime' provides classes for embedding partial missingness as a central part of its datetime classes. This central feature allows for more ergonomic use of datetimes for challenging datetime computation, including calculations of overlapping date ranges, imputations, and more thoughtful handling of ambiguity that arises from uncertain time zones. This package was developed first and foremost with pharmaceutical applications in mind, but aims to be agnostic to application to accommodate general use cases just as conveniently.

Maintained by Doug Kelkhoff. Last updated 1 years ago.

hacktoberfest

17 stars 3.93 score 3 scripts

ralmond

EIEvent:Evidence Identification Event Processing Engine

Extracts observables from a sequence of events. Uses a prolog-like rule language to do the extraction, written in JSON.

Maintained by Russell Almond. Last updated 1 years ago.

assessment-scoring evidence-centered-design

2.00 score 2 scripts