Showing 35 of total 35 results (show query)
bioc
Biobase:Biobase: Base functions for Bioconductor
Functions that are needed by many other packages or which replace R functions.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
infrastructurebioconductor-packagecore-package
9 stars 16.45 score 6.6k scripts 1.8k dependents
r-lib
desc:Manipulate DESCRIPTION Files
Tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.
Maintained by Gábor Csárdi. Last updated 2 months ago.
123 stars 14.68 score 409 scripts 1.1k dependentsbioc
MSnbase:Base Functions and Classes for Mass Spectrometry and Proteomics
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
Maintained by Laurent Gatto. Last updated 15 days ago.
immunooncologyinfrastructureproteomicsmassspectrometryqualitycontroldataimportbioconductorbioinformaticsmass-spectrometryproteomics-datavisualisationcpp
131 stars 12.76 score 772 scripts 36 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 25 days ago.
419 stars 12.39 score 448 scripts 8 dependents
melff
memisc:Management of Survey Data and Presentation of Analysis Results
An infrastructure for the management of survey data including value labels, definable missing values, recoding of variables, production of code books, and import of (subsets of) 'SPSS' and 'Stata' files is provided. Further, the package allows to produce tables and data frames of arbitrary descriptive statistics and (almost) publication-ready tables of regression model estimates, which can be exported to 'LaTeX' and HTML.
Maintained by Martin Elff. Last updated 24 days ago.
46 stars 12.34 score 1.2k scripts 13 dependents
crunch-io
crunch:Crunch.io Data Tools
The Crunch.io service <https://crunch.io/> provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
Maintained by Greg Freedman Ellis. Last updated 8 days ago.
9 stars 10.47 score 200 scripts 2 dependentsbioc
GSEABase:Gene set enrichment data structures and methods
This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).
Maintained by Bioconductor Package Maintainer. Last updated 2 months ago.
geneexpressiongenesetenrichmentgraphandnetworkgokegg
10.27 score 1.5k scripts 77 dependentsbioc
flowCore:flowCore: Basic structures for flow cytometry data
Provides S4 data structures and basic functions to deal with flow cytometry data.
Maintained by Mike Jiang. Last updated 5 months ago.
immunooncologyinfrastructureflowcytometrycellbasedassayscpp
10.17 score 1.7k scripts 59 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
mhahsler
stream:Infrastructure for Data Stream Mining
A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893, NSF CMMI 1728612, and NIH R21HG005912. Hahsler et al (2017) <doi:10.18637/jss.v076.i14>.
Maintained by Michael Hahsler. Last updated 17 days ago.
data-stream-clusteringdatastreamstream-miningcpp
39 stars 10.05 score 132 scripts 3 dependentsbioc
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.
softwareinfrastructuredataimportdatarepresentationhic
7 stars 9.31 score 162 scripts 5 dependentsbioc
topGO:Enrichment Analysis for Gene Ontology
topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.
Maintained by Adrian Alexa. Last updated 5 months ago.
8.96 score 2.0k scripts 20 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.
1 stars 8.35 score 358 scripts 70 dependents
r-world-devs
cohortBuilder:Data Source Agnostic Filtering Tools
Common API for filtering data stored in different data models. Provides multiple filter types and reproducible R code. Works standalone or with 'shinyCohortBuilder' as the GUI for interactive Shiny apps.
Maintained by Krystian Igras. Last updated 11 days ago.
8 stars 8.01 score 55 scripts 1 dependentsbioc
Category:Category Analysis
A collection of tools for performing category (gene set enrichment) analysis.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
annotationgopathwaysgenesetenrichment
7.93 score 183 scripts 16 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
dataobservatory-eu
dataset:Create Data Frames that are Easier to Exchange and Reuse
The aim of the 'dataset' package is to make tidy datasets easier to release, exchange and reuse. It organizes and formats data frame 'R' objects into well-referenced, well-described, interoperable datasets into release and reuse ready form.
Maintained by Daniel Antal. Last updated 4 days ago.
14 stars 7.89 score 76 scripts 1 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
ekstroem
dataMaid:A Suite of Checks for Identification of Potential Errors in a Data Frame as Part of the Data Screening Process
Data screening is an important first step of any statistical analysis. dataMaid auto generates a customizable data report with a thorough summary of the checks and the results that a human can use to identify possible errors. It provides an extendable suite of test for common potential errors in a dataset.
Maintained by Claus Thorn Ekstrøm. Last updated 3 years ago.
data-cleaningdata-screeningreproducible-research
143 stars 7.53 score 236 scripts
syncrosim
rsyncrosim:The R Interface to 'SyncroSim'
'SyncroSim' is a generalized framework for managing scenario-based datasets (<https://syncrosim.com/>). 'rsyncrosim' provides an interface to 'SyncroSim'. Simulation models can be added to 'SyncroSim' in order to transform these datasets, taking advantage of general features such as defining scenarios of model inputs, running Monte Carlo simulations, and summarizing model outputs. 'rsyncrosim' requires 'SyncroSim' 2.3.5 or higher (API documentation: <https://docs.syncrosim.com/>).
Maintained by Katie Birchard. Last updated 22 days ago.
9 stars 7.09 score 189 scripts
khliland
baseline:Baseline Correction of Spectra
Collection of baseline correction algorithms, along with a framework and a Tcl/Tk enabled GUI for optimising baseline algorithm parameters. Typical use of the package is for removing background effects from spectra originating from various types of spectroscopy and spectrometry, possibly optimizing this with regard to regression or classification results. Correction methods include polynomial fitting, weighted local smoothers and many more.
Maintained by Kristian Hovde Liland. Last updated 10 months ago.
9 stars 7.07 score 74 scripts 12 dependentsbioc
GOstats:Tools for manipulating GO and microarrays
A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
annotationgomultiplecomparisongeneexpressionmicroarraypathwaysgenesetenrichmentgraphandnetwork
6.93 score 528 scripts 12 dependentsdata-cleaning
dcmodify:Modify Data Using Externally Defined Modification Rules
Data cleaning scripts typically contain a lot of 'if this change that' type of statements. Such statements are typically condensed expert knowledge. With this package, such 'data modifying rules' are taken out of the code and become in stead parameters to the work flow. This allows one to maintain, document, and reason about data modification rules as separate entities.
Maintained by Mark van der Loo. Last updated 10 months ago.
10 stars 6.24 score 58 scriptsekstroem
dataReporter:Reproducible Data Screening Checks and Report of Possible Errors
Data screening is an important first step of any statistical analysis. 'dataReporter' auto generates a customizable data report with a thorough summary of the checks and the results that a human can use to identify possible errors. It provides an extendable suite of test for common potential errors in a dataset. See Petersen AH, Ekstrøm CT (2019). "dataMaid: Your Assistant for Documenting Supervised Data Quality Screening in R." _Journal of Statistical Software_, *90*(6), 1-38 <doi:10.18637/jss.v090.i06> for more information.
Maintained by Claus Thorn Ekstrøm. Last updated 2 years ago.
86 stars 6.16 score 34 scriptsbioc
qcmetrics:A Framework for Quality Control
The package provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.
Maintained by Laurent Gatto. Last updated 5 months ago.
immunooncologysoftwarequalitycontrolproteomicsmicroarraymassspectrometryvisualizationreportwriting
2 stars 6.03 score 2 dependents
cox-labs
PerseusR:Perseus R Interop
Enables the interoperability between the Perseus platform for omics data analysis (Tyanova et al. 2016) <doi:10.1038/nmeth.3901> and R. It provides the foundation for developing and running Perseus plugins implemented in R by providing all required input and output handling, including data and parameter parsing as described in Rudolph and Cox 2018 <doi:10.1101/447268>.
Maintained by Jan Rudolph. Last updated 3 years ago.
bioinformaticsinteropmaxquantperseusproteomics
13 stars 5.88 score 58 scripts
eltoulemonde
dataPreparation:Automated Data Preparation
Do most of the painful data preparation for a data science project with a minimum amount of code; Take advantages of 'data.table' efficiency and use some algorithmic trick in order to perform data preparation in a time and RAM efficient way.
Maintained by Emmanuel-Lin Toulemonde. Last updated 2 years ago.
data-preparationdata-preprocessingdata-sciencedate-conversionspeedvariable-eliminationvariable-selection
31 stars 5.44 score 86 scripts
husson
FactoInvestigate:Automatic Description of Factorial Analysis
Brings a set of tools to help and automatically realise the description of principal component analyses (from 'FactoMineR' functions). Detection of existing outliers, identification of the informative components, graphical views and dimensions description are performed threw dedicated functions. The Investigate() function performs all these functions in one, and returns the result as a report document (Word, PDF or HTML).
Maintained by Francois Husson. Last updated 2 years ago.
1 stars 4.90 score 68 scripts 1 dependents
aberhrml
metaboData:Example Metabolomics Data Sets
Data sets from a variety of biological sample matrices, analysed using a number of mass spectrometry based metabolomic analytical techniques. The example data sets are stored remotely using GitHub releases <https://github.com/aberHRML/metaboData/releases> which can be accessed from R using the package. The package also includes the 'abr1' FIE-MS data set from the 'FIEmspro' package <https://users.aber.ac.uk/jhd/> <doi:10.1038/nprot.2007.511>.
Maintained by Jasen Finch. Last updated 3 years ago.
datadatasetsfie-hrmsfie-msmass-spectrometrymetabolomics
1 stars 4.72 score 104 scripts
robinhankin
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 scriptsbioc
loci2path:Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
loci2path performs statistics-rigorous enrichment analysis of eQTLs in genomic regions of interest. Using eQTL collections provided by the Genotype-Tissue Expression (GTEx) project and pathway collections from MSigDB.
Maintained by Tianlei Xu. Last updated 5 months ago.
functionalgenomicsgeneticsgenesetenrichmentsoftwaregeneexpressionsequencingcoveragebiocarta
1 stars 4.30 score 2 scripts
simon-lenau
prolific.api:A User-Friendly Interface for Accessing the Prolific API
A user-friendly interface for creating and managing empirical crowd-sourcing studies via API access to <https://www.prolific.co>.
Maintained by Simon Lenau. Last updated 2 years ago.
crowd-sourcingcrowdsourcing-experimentscrowdsourcing-platformsempirical-researchparticipantssampling
3.70 score 8 scriptscran
Rdiagnosislist:Manipulate SNOMED CT Diagnosis Lists
Functions and methods for manipulating 'SNOMED CT' concepts. The package contains functions for loading the 'SNOMED CT' release into a convenient R environment, selecting 'SNOMED CT' concepts using regular expressions, and navigating the 'SNOMED CT' ontology. It provides the 'SNOMEDconcept' S3 class for a vector of 'SNOMED CT' concepts (stored as 64-bit integers) and the 'SNOMEDcodelist' S3 class for a table of concepts IDs with descriptions. The package can be used to construct sets of 'SNOMED CT' concepts for research (<doi:10.1093/jamia/ocac158>). For more information about 'SNOMED CT' visit <https://www.snomed.org/>.
Maintained by Anoop D. Shah. Last updated 2 months ago.
1 stars 3.60 scorecran
tis:Time Indexes and Time Indexed Series
Functions and S3 classes for time indexes and time indexed series, which are compatible with FAME frequencies.
Maintained by Brian Salzer. Last updated 4 years ago.
3.35 score 6 dependentscran
synchronicity:Boost Mutex Functionality in R
Boost mutex functionality in R.
Maintained by Michael J. Kane. Last updated 1 years ago.
2.64 score 2 dependents