Showing 34 of total 34 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
harrelfe
Hmisc:Harrell Miscellaneous
Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, simulation, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, recoding variables, caching, simplified parallel computing, encrypting and decrypting data using a safe workflow, general moving window statistical estimation, and assistance in interpreting principal component analysis.
Maintained by Frank E Harrell Jr. Last updated 4 days ago.
209 stars 17.64 score 17k scripts 750 dependents
tidymodels
parsnip:A Common API to Modeling and Analysis Functions
A common interface is provided to allow users to specify a model without having to remember the different argument names across different functions or computational engines (e.g. 'R', 'Spark', 'Stan', 'H2O', etc).
Maintained by Max Kuhn. Last updated 17 days ago.
612 stars 16.37 score 3.4k scripts 69 dependentsbioc
EBImage:Image processing and analysis toolbox for R
EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.
Maintained by Andrzej Oleś. Last updated 5 months ago.
visualizationbioinformaticsimage-analysisimage-processingcpp
71 stars 12.77 score 1.5k scripts 33 dependents
ohdsi
SqlRender:Rendering Parameterized SQL and Translation to Dialects
A rendering tool for parameterized SQL that also translates into different SQL dialects. These dialects include 'Microsoft SQL Server', 'Oracle', 'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', 'Snowflake', 'Azure Synapse Analytics Dedicated', 'Apache Spark', 'SQLite', and 'InterSystems IRIS'.
Maintained by Martijn Schuemie. Last updated 16 days ago.
82 stars 12.52 score 488 scripts 13 dependents
paws-r
paws:Amazon Web Services Software Development Kit
Interface to Amazon Web Services <https://aws.amazon.com>, including storage, database, and compute services, such as 'Simple Storage Service' ('S3'), 'DynamoDB' 'NoSQL' database, and 'Lambda' functions-as-a-service.
Maintained by Dyfan Jones. Last updated 16 days ago.
332 stars 11.25 score 177 scripts 12 dependents
bioc
SpatialFeatureExperiment:Integrating SpatialExperiment with Simple Features in sf
A new S4 class integrating Simple Features with the R package sf to bring geospatial data analysis methods based on vector data to spatial transcriptomics. Also implements management of spatial neighborhood graphs and geometric operations. This pakage builds upon SpatialExperiment and SingleCellExperiment, hence methods for these parent classes can still be used.
Maintained by Lambda Moses. Last updated 2 months ago.
datarepresentationtranscriptomicsspatial
49 stars 9.40 score 322 scripts 1 dependentspaws-r
paws.machine.learning:'Amazon Web Services' Machine Learning Services
Interface to 'Amazon Web Services' machine learning services, including 'SageMaker' managed machine learning service, natural language processing, speech recognition, translation, and more <https://aws.amazon.com/machine-learning/>.
Maintained by Dyfan Jones. Last updated 16 days ago.
332 stars 9.05 score 14 dependents
thomasp85
ambient:A Generator of Multidimensional Noise
Generation of natural looking noise has many application within simulation, procedural generation, and art, to name a few. The 'ambient' package provides an interface to the 'FastNoise' C++ library and allows for efficient generation of perlin, simplex, worley, cubic, value, and white noise with optional perturbation in either 2, 3, or 4 (in case of simplex and white noise) dimensions.
Maintained by Thomas Lin Pedersen. Last updated 3 years ago.
97 stars 8.09 score 956 scripts 2 dependents
jonclayden
RNiftyReg:Image Registration Using the 'NiftyReg' Library
Provides an 'R' interface to the 'NiftyReg' image registration tools <https://github.com/KCL-BMEIS/niftyreg>. Linear and nonlinear registration are supported, in two and three dimensions.
Maintained by Jon Clayden. Last updated 6 months ago.
image-registrationmedical-imagingtransformationscppopenmp
43 stars 7.69 score 50 scripts 5 dependents
dusadrian
admisc:Adrian Dusa's Miscellaneous
Contains functions used across packages 'DDIwR', 'QCA' and 'venn'. Interprets and translates, factorizes and negates SOP - Sum of Products expressions, for both binary and multi-value crisp sets, and extracts information (set names, set values) from those expressions. Other functions perform various other checks if possibly numeric (even if all numbers reside in a character vector) and coerce to numeric, or check if the numbers are whole. It also offers, among many others, a highly versatile recoding routine and some more flexible alternatives to the base functions 'with()' and 'within()'. SOP simplification functions in this package use related minimization from package 'QCA', which is recommended to be installed despite not being listed in the Imports field, due to circular dependency issues.
Maintained by Adrian Dusa. Last updated 16 days ago.
2 stars 7.61 score 20 scripts 92 dependents
biogenies
tidysq:Tidy Processing and Analysis of Biological Sequences
A tidy approach to analysis of biological sequences. All processing and data-storage functions are heavily optimized to allow the fastest and most efficient data storage.
Maintained by Dominik Rafacz. Last updated 3 months ago.
bioconductorbioinformaticsbiological-sequencesfastas3sequencestibbletidytidyversevctrscpp
40 stars 7.56 score 38 scripts
mschubert
narray:Subset- And Name-Aware Array Utility Functions
Stacking arrays according to dimension names, subset-aware splitting and mapping of functions, intersecting along arbitrary dimensions, converting to and from data.frames, and many other helper functions.
Maintained by Michael Schubert. Last updated 2 months ago.
27 stars 6.91 score 10 scripts 10 dependentsbioc
bioCancer:Interactive Multi-Omics Cancers Data Visualization and Analysis
This package is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.
Maintained by Karim Mezhoud. Last updated 5 months ago.
guidatarepresentationnetworkmultiplecomparisonpathwaysreactomevisualizationgeneexpressiongenetargetanalysisbiocancer-interfacecancercancer-studiesrmarkdown
20 stars 5.78 score 7 scripts
zumbov2
deeplr:Interface to the 'DeepL' Translation API
A wrapper for the 'DeepL' Pro API <https://www.deepl.com/docs-api>, a web service for translating texts between different languages. A DeepL API developer account is required to use the service (see <https://www.deepl.com/pro#developer>).
Maintained by David Zumbach. Last updated 1 years ago.
41 stars 5.56 score 70 scripts
yulab-smu
fanyi:Translate Words or Sentences via Online Translators
Useful functions to translate text for multiple languages using online translators. For example, by translating error messages and descriptive analysis results into a language familiar to the user, it enables a better understanding of the information, thereby reducing the barriers caused by language. It offers several helper functions to query gene information to help interpretation of interested genes (e.g., marker genes, differential expression genes), and provides utilities to translate 'ggplot' graphics. This package is not affiliated with any of the online translators. The developers do not take responsibility for the invoice it incurs when using this package, especially for exceeding the free quota.
Maintained by Guangchuang Yu. Last updated 4 months ago.
52 stars 5.49 score 10 scripts
larssnip
microseq:Basic Biological Sequence Handling
Basic functions for microbial sequence data analysis. The idea is to use generic R data structures as much as possible, making R data wrangling possible also for sequence data.
Maintained by Lars Snipen. Last updated 10 months ago.
3 stars 5.46 score 54 scripts 3 dependents
icosa-grid
icosa:Global Triangular and Penta-Hexagonal Grids Based on Tessellated Icosahedra
Implementation of icosahedral grids in three dimensions. The spherical-triangular tessellation can be set to create grids with custom resolutions. Both the primary triangular and their inverted penta-hexagonal grids can be calculated. Additional functions are provided that allow plotting of the grids and associated data, the interaction of the grids with other raster and vector objects, and treating the grids as a graphs.
Maintained by Adam T. Kocsis. Last updated 8 months ago.
4 stars 5.41 score 65 scriptsbioc
miRNAtap:miRNAtap: microRNA Targets - Aggregated Predictions
The package facilitates implementation of workflows requiring miRNA predictions, it allows to integrate ranked miRNA target predictions from multiple sources available online and aggregate them with various methods which improves quality of predictions above any of the single sources. Currently predictions are available for Homo sapiens, Mus musculus and Rattus norvegicus (the last one through homology translation).
Maintained by T. Ian Simpson. Last updated 5 months ago.
softwareclassificationmicroarraysequencingmirna
4.94 score 44 scripts
mattheaphy
offsetreg:An Extension of 'Tidymodels' Supporting Offset Terms
Extend the 'tidymodels' ecosystem <https://www.tidymodels.org/> to enable the creation of predictive models with offset terms. Models with offsets are most useful when working with count data or when fitting an adjustment model on top of an existing model with a prior expectation. The former situation is common in insurance where data is often weighted by exposures. The latter is common in life insurance where industry mortality tables are often used as a starting point for setting assumptions.
Maintained by Matt Heaphy. Last updated 1 months ago.
2 stars 4.48 score 4 scripts
jlp-bioinf
RRNA:Secondary Structure Plotting for RNA
Functions for creating and manipulating RNA secondary structure plots.
Maintained by JP Bida. Last updated 11 months ago.
1 stars 4.33 score 47 scripts 1 dependentsbioc
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.
mathematicalbiologycomparativegenomicsfunctionalgenomicsmultiplesequencealignmentwholegenomegenetic-codegenetic-code-algebragenomegenome-algebra
4.30 score 9 scripts
kurthornik
tau:Text Analysis Utilities
Utilities for text analysis.
Maintained by Kurt Hornik. Last updated 6 months ago.
4.02 score 115 scripts 6 dependents
chuxinyuan
ecce:Translate English Sentence into Chinese, or Translate Chinese Sentence into English
If translate English or Chinese sentence, there is a faster way for R user. You can pass in an English or Chinese sentence, ecce package support both English and Chinese translation. It also support browse translation results in website. In addition, also support obtain the pinyin of the Chinese character, you can more easily understand the pronunciation of the Chinese character.
Maintained by Xinyuan Chu. Last updated 9 months ago.
4.00 score 4 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
cloudyr
aws.translate:Client for 'AWS Translate'
A client for 'AWS Translate' <https://aws.amazon.com/documentation/translate>, a machine translation service that will convert a text input in one language into a text output in another language.
Maintained by Antoine Sachet. Last updated 5 years ago.
awsaws-translatecloudyrmachine-translation
2 stars 3.48 score 4 scripts
mohamed-180
gtranslate:Translate Between Different Languages
The goal of this package is to translate between different languages without any Google API authentication which is pain and you must pay for the key, This package is free and lightweight.
Maintained by Mohamed El-Desouky. Last updated 2 years ago.
4 stars 3.30 score 7 scripts
matt-dray
r2eng:Translate R Code To An English Sentence
Take an R expression and convert it to English by matching recognised symbols with an opinionated list of English 'translations'. Inspired By Amelia McNamara's useR! 2020 conference talk.
Maintained by Matt Dray. Last updated 11 months ago.
17 stars 2.93 score 6 scripts
rosawojciech
rcube:Simulations and Visualizations of Rubik's Cube (with Mods)
Provides simplified methods for managing classic Rubik's cubes and many other modifications of it (such as NxNxN size cubes, void cubes and 8-coloured cubes - so called octa cubes). Includes functions of handling special syntax for managing such cubes; and different approach to plotting 3D cubes without using external libraries (for example 'OpenGL').
Maintained by Wojciech Rosa. Last updated 6 years ago.
2.70 score 9 scripts
gertstulp
FertNet:Process Data from the Social Networks and Fertility Survey
Processes data from The Social Networks and Fertility Survey, downloaded from <https://dataarchive.lissdata.nl>, including correcting respondent errors and transforming network data into network objects to facilitate analyses and visualisation.
Maintained by Gert Stulp. Last updated 11 months ago.
2.70 score 2 scripts
philippallmann
jocre:Joint Confidence Regions
Computing and plotting joint confidence regions and intervals. Regions include classical ellipsoids, minimum-volume or minimum-length regions, and an empirical Bayes region. Intervals include the TOST procedure with ordinary or expanded intervals and a fixed-sequence procedure. Such regions and intervals are useful e.g., for the assessment of multi-parameter (bio-)equivalence. Joint confidence regions for the mean and variance of a normal distribution are available as well.
Maintained by Philip Pallmann. Last updated 8 years ago.
1 stars 2.00 score 9 scripts
cran
tmplate:Code Generation Based on Templates
Define general templates with tags that can be replaced by content depending on arguments and objects to modify the final output of the document.
Maintained by Mario A. Martinez Araya. Last updated 4 years ago.
2.00 score