Showing 192 of total 192 results (show query)
tidyverse
tidyverse:Easily Install and Load the 'Tidyverse'
The 'tidyverse' is a set of packages that work in harmony because they share common data representations and 'API' design. This package is designed to make it easy to install and load multiple 'tidyverse' packages in a single step. Learn more about the 'tidyverse' at <https://www.tidyverse.org>.
Maintained by Hadley Wickham. Last updated 5 months ago.
1.7k stars 20.23 score 664k scripts 125 dependentstidyverse
googledrive:An Interface to Google Drive
Manage Google Drive files from R.
Maintained by Jennifer Bryan. Last updated 8 months ago.
329 stars 14.97 score 2.1k scripts 164 dependentstidyverse
googlesheets4:Access Google Sheets using the Sheets API V4
Interact with Google Sheets through the Sheets API v4 <https://developers.google.com/sheets/api>. "API" is an acronym for "application programming interface"; the Sheets API allows users to interact with Google Sheets programmatically, instead of via a web browser. The "v4" refers to the fact that the Sheets API is currently at version 4. This package can read and write both the metadata and the cell data in a Sheet.
Maintained by Jennifer Bryan. Last updated 8 months ago.
google-drivegoogle-sheetsspreadsheet
363 stars 14.55 score 7.0k scripts 142 dependents
markedmondson1234
googleAuthR:Authenticate and Create Google APIs
Create R functions that interact with OAuth2 Google APIs <https://developers.google.com/apis-explorer/> easily, with auto-refresh and Shiny compatibility.
Maintained by Erik Grönroos. Last updated 10 months ago.
apiauthenticationgooglegoogleauthroauth2-flowshiny
178 stars 12.85 score 804 scripts 13 dependents
r-dbi
bigrquery:An Interface to Google's 'BigQuery' 'API'
Easily talk to Google's 'BigQuery' database from R.
Maintained by Hadley Wickham. Last updated 1 months ago.
520 stars 12.47 score 1.8k scripts 4 dependents
r-lib
gmailr:Access the 'Gmail' 'RESTful' API
An interface to the 'Gmail' 'RESTful' API. Allows access to your 'Gmail' messages, threads, drafts and labels.
Maintained by Jennifer Bryan. Last updated 1 years ago.
230 stars 11.50 score 289 scripts 1 dependents
ropensci
googleLanguageR:Call Google's 'Natural Language' API, 'Cloud Translation' API, 'Cloud Speech' API and 'Cloud Text-to-Speech' API
Call 'Google Cloud' machine learning APIs for text and speech tasks. Call the 'Cloud Translation' API <https://cloud.google.com/translate/> for detection and translation of text, the 'Natural Language' API <https://cloud.google.com/natural-language/> to analyse text for sentiment, entities or syntax, the 'Cloud Speech' API <https://cloud.google.com/speech/> to transcribe sound files to text and the 'Cloud Text-to-Speech' API <https://cloud.google.com/text-to-speech/> to turn text into sound files.
Maintained by Mark Edmondson. Last updated 9 months ago.
cloud-speech-apicloud-translation-apigoogle-api-clientgoogle-cloudgoogle-cloud-speechgoogle-nlpgoogleauthrnatural-language-processingpeer-reviewedsentiment-analysisspeech-apitranslation-api
196 stars 10.36 score 268 scripts 3 dependents
cloudyr
googleCloudStorageR:Interface with Google Cloud Storage API
Interact with Google Cloud Storage <https://cloud.google.com/storage/> API in R. Part of the 'cloudyr' <https://cloudyr.github.io/> project.
Maintained by Mark Edmondson. Last updated 19 days ago.
apiapi-clientgoogle-cloud-storagegoogleauthr
104 stars 10.28 score 548 scripts 1 dependents
idigbio
ridigbio:Interface to the iDigBio Data API
An interface to iDigBio's search API that allows downloading specimen records. Searches are returned as a data.frame. Other functions such as the metadata end points return lists of information. iDigBio is a US project focused on digitizing and serving museum specimen collections on the web. See <https://www.idigbio.org> for information on iDigBio.
Maintained by Jesse Bennett. Last updated 20 days ago.
16 stars 10.23 score 63 scripts 7 dependents
8-bit-sheep
googleAnalyticsR:Google Analytics API into R
Interact with the Google Analytics APIs <https://developers.google.com/analytics/>, including the Core Reporting API (v3 and v4), Management API, User Activity API GA4's Data API and Admin API and Multi-Channel Funnel API.
Maintained by Erik Grönroos. Last updated 7 months ago.
analyticsapigooglegoogleanalyticsrgoogleauthr
262 stars 10.11 score 680 scripts 1 dependentsropensci
spocc:Interface to Species Occurrence Data Sources
A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'iNaturalist', 'eBird', Integrated Digitized 'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes functionality for retrieving species occurrence data, and combining those data.
Maintained by Hannah Owens. Last updated 2 months ago.
specimensapiweb-servicesoccurrencesspeciestaxonomygbifinatvertnetebirdidigbioobisalaantwebbisondataecoengineinaturalistoccurrencespecies-occurrencespocc
118 stars 10.09 score 552 scripts 5 dependentscloudyr
googleComputeEngineR:R Interface with Google Compute Engine
Interact with the 'Google Compute Engine' API in R. Lets you create, start and stop instances in the 'Google Cloud'. Support for preconfigured instances, with templates for common R needs.
Maintained by Mark Edmondson. Last updated 16 days ago.
apicloud-computingcloudyrgoogle-cloudgoogleauthrlaunching-virtual-machines
152 stars 9.73 score 235 scripts
bioc
BatchQC:Batch Effects Quality Control Software
Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. BatchQC is a software tool that streamlines batch preprocessing and evaluation by providing interactive diagnostics, visualizations, and statistical analyses to explore the extent to which batch variation impacts the data. BatchQC diagnostics help determine whether batch adjustment needs to be done, and how correction should be applied before proceeding with a downstream analysis. Moreover, BatchQC interactively applies multiple common batch effect approaches to the data and the user can quickly see the benefits of each method. BatchQC is developed as a Shiny App. The output is organized into multiple tabs and each tab features an important part of the batch effect analysis and visualization of the data. The BatchQC interface has the following analysis groups: Summary, Differential Expression, Median Correlations, Heatmaps, Circular Dendrogram, PCA Analysis, Shape, ComBat and SVA.
Maintained by Jessica Anderson. Last updated 13 days ago.
batcheffectgraphandnetworkmicroarraynormalizationprincipalcomponentsequencingsoftwarevisualizationqualitycontrolrnaseqpreprocessingdifferentialexpressionimmunooncology
7 stars 9.06 score 54 scripts
claudiozandonella
trackdown:Collaborative Editing of Rmd (or Quarto / Rnw) Documents in Google Drive
Collaborative writing and editing of R Markdown (or Quarto / Sweave) documents. The local .Rmd (or Quarto / .Rnw) is uploaded as a plain-text file to Google Drive. By taking advantage of the easily readable Markdown (or LaTeX) syntax and the well-known online interface offered by Google Docs, collaborators can easily contribute to the writing and editing process. After integrating all authors’ contributions, the final document can be downloaded and rendered locally.
Maintained by Claudio Zandonella Callegher. Last updated 2 years ago.
222 stars 8.49 score 69 scripts
wallaceecomod
wallace:A Modular Platform for Reproducible Modeling of Species Niches and Distributions
The 'shiny' application Wallace is a modular platform for reproducible modeling of species niches and distributions. Wallace guides users through a complete analysis, from the acquisition of species occurrence and environmental data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface. An extensive vignette, which guides users through most package functionality can be found on the package's GitHub Pages website: <https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html>.
Maintained by Mary E. Blair. Last updated 24 days ago.
133 stars 8.36 score 96 scripts
flavjack
inti:Tools and Statistical Procedures in Plant Science
The 'inti' package is part of the 'inkaverse' project for developing different procedures and tools used in plant science and experimental designs. The mean aim of the package is to support researchers during the planning of experiments and data collection (tarpuy()), data analysis and graphics (yupana()) , and technical writing. Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Maintained by Flavio Lozano-Isla. Last updated 16 days ago.
agricultureappsinkaverselmmplant-breedingplant-scienceshiny
5 stars 8.27 score 193 scripts
proteomicslab57357
UniprotR:Retrieving Information of Proteins from Uniprot
Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information, For detailed information kindly read the publication <https://www.sciencedirect.com/science/article/pii/S1874391919303859>.
Maintained by Mohamed Soudy. Last updated 3 years ago.
61 stars 7.65 score 89 scripts 1 dependents
jhudsl
ari:Automated R Instructor
Create videos from 'R Markdown' documents, or images and audio files. These images can come from image files or HTML slides, and the audio files can be provided by the user or computer voice narration can be created using 'Amazon Polly'. The purpose of this package is to allow users to create accessible, translatable, and reproducible lecture videos. See <https://aws.amazon.com/polly/> for more information.
Maintained by Sean Kross. Last updated 2 years ago.
147 stars 7.43 score 41 scripts 1 dependents
eltebioinformatics
mulea:Enrichment Analysis Using Multiple Ontologies and False Discovery Rate
Background - Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce mulea, an R package offering comprehensive overrepresentation and functional enrichment analysis. Results - mulea employs a progressive empirical false discovery rate (eFDR) method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies. mulea expands beyond traditional tools by incorporating a wide range of ontologies, encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility enables researchers to tailor enrichment analysis to their specific questions, such as identifying enriched transcriptional regulators in gene expression data or overrepresented protein domains in protein sets. To facilitate seamless analysis, mulea provides gene sets (in standardised GMT format) for 27 model organisms, covering 22 ontology types from 16 databases and various identifiers resulting in almost 900 files. Additionally, the muleaData ExperimentData Bioconductor package simplifies access to these pre-defined ontologies. Finally, mulea's architecture allows for easy integration of user-defined ontologies, or GMT files from external sources (e.g., MSigDB or Enrichr), expanding its applicability across diverse research areas. Conclusions - mulea is distributed as a CRAN R package. It offers researchers a powerful and flexible toolkit for functional enrichment analysis, addressing limitations of traditional tools with its progressive eFDR and by supporting a variety of ontologies. Overall, mulea fosters the exploration of diverse biological questions across various model organisms.
Maintained by Tamas Stirling. Last updated 4 months ago.
annotationdifferentialexpressiongeneexpressiongenesetenrichmentgographandnetworkmultiplecomparisonpathwaysreactomesoftwaretranscriptionvisualizationenrichmentenrichment-analysisfunctional-enrichment-analysisgene-set-enrichmentontologiestranscriptomicscpp
28 stars 7.36 score 34 scripts
usaid-oha-si
glamr:SI Utilities Package
Provides a series of base functions useful to the GH OHA SI team. This includes project setup, pulling from DATIM, and key functions for working with the MSD.
Maintained by Aaron Chafetz. Last updated 6 months ago.
2 stars 7.20 score 1.3k scripts 1 dependents
roux-ohdsi
allofus:Interface for 'All of Us' Researcher Workbench
Streamline use of the 'All of Us' Researcher Workbench (<https://www.researchallofus.org/data-tools/workbench/>)with tools to extract and manipulate data from the 'All of Us' database. Increase interoperability with the Observational Health Data Science and Informatics ('OHDSI') tool stack by decreasing reliance of 'All of Us' tools and allowing for cohort creation via 'Atlas'. Improve reproducible and transparent research using 'All of Us'.
Maintained by Rob Cavanaugh. Last updated 5 months ago.
16 stars 7.19 score 30 scriptsbioc
musicatk:Mutational Signature Comprehensive Analysis Toolkit
Mutational signatures are carcinogenic exposures or aberrant cellular processes that can cause alterations to the genome. We created musicatk (MUtational SIgnature Comprehensive Analysis ToolKit) to address shortcomings in versatility and ease of use in other pre-existing computational tools. Although many different types of mutational data have been generated, current software packages do not have a flexible framework to allow users to mix and match different types of mutations in the mutational signature inference process. Musicatk enables users to count and combine multiple mutation types, including SBS, DBS, and indels. Musicatk calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type. Musicatk also implements several methods for discovery of new signatures as well as methods to infer exposure given an existing set of signatures. Musicatk provides functions for visualization and downstream exploratory analysis including the ability to compare signatures between cohorts and find matching signatures in COSMIC V2 or COSMIC V3.
Maintained by Joshua D. Campbell. Last updated 5 months ago.
softwarebiologicalquestionsomaticmutationvariantannotation
13 stars 6.97 score 20 scripts
cmerow
rangeModelMetadata:Provides Templates for Metadata Files Associated with Species Range Models
Range Modeling Metadata Standards (RMMS) address three challenges: they (i) are designed for convenience to encourage use, (ii) accommodate a wide variety of applications, and (iii) are extensible to allow the community of range modelers to steer it as needed. RMMS are based on a data dictionary that specifies a hierarchical structure to catalog different aspects of the range modeling process. The dictionary balances a constrained, minimalist vocabulary to improve standardization with flexibility for users to provide their own values. Merow et al. (2019) <DOI:10.1111/geb.12993> describe the standards in more detail. Note that users who prefer to use the R package 'ecospat' can obtain it from <https://github.com/ecospat/ecospat>.
Maintained by Cory Merow. Last updated 9 months ago.
ecological-metadata-languageecological-modellingecological-modelsecologyspecies-distribution-modellingspecies-distributions
6 stars 6.96 score 16 scripts 3 dependents
danlwarren
ENMTools:Analysis of Niche Evolution using Niche and Distribution Models
Constructing niche models and analyzing patterns of niche evolution. Acts as an interface for many popular modeling algorithms, and allows users to conduct Monte Carlo tests to address basic questions in evolutionary ecology and biogeography. Warren, D.L., R.E. Glor, and M. Turelli (2008) <doi:10.1111/j.1558-5646.2008.00482.x> Glor, R.E., and D.L. Warren (2011) <doi:10.1111/j.1558-5646.2010.01177.x> Warren, D.L., R.E. Glor, and M. Turelli (2010) <doi:10.1111/j.1600-0587.2009.06142.x> Cardillo, M., and D.L. Warren (2016) <doi:10.1111/geb.12455> D.L. Warren, L.J. Beaumont, R. Dinnage, and J.B. Baumgartner (2019) <doi:10.1111/ecog.03900>.
Maintained by Dan Warren. Last updated 3 months ago.
105 stars 6.91 score 126 scripts
raymondbalise
rUM:R Templates from the University of Miami
This holds some r markdown and quarto templates and a template to create a research project in "R Studio".
Maintained by Raymond Balise. Last updated 10 days ago.
9 stars 6.84 score 16 scripts
hegghammer
daiR:Interface with Google Cloud Document AI API
R interface for the Google Cloud Services 'Document AI API' <https://cloud.google.com/document-ai/> with additional tools for output file parsing and text reconstruction. 'Document AI' is a powerful server-based OCR service that extracts text and tables from images and PDF files with high accuracy. 'daiR' gives R users programmatic access to this service and additional tools to handle and visualize the output. See the package website <https://dair.info/> for more information and examples.
Maintained by Thomas Hegghammer. Last updated 5 months ago.
42 stars 6.77 score 40 scriptsbioc
SPONGE:Sparse Partial Correlations On Gene Expression
This package provides methods to efficiently detect competitive endogeneous RNA interactions between two genes. Such interactions are mediated by one or several miRNAs such that both gene and miRNA expression data for a larger number of samples is needed as input. The SPONGE package now also includes spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.
Maintained by Markus List. Last updated 5 months ago.
geneexpressiontranscriptiongeneregulationnetworkinferencetranscriptomicssystemsbiologyregressionrandomforestmachinelearning
6.66 score 38 scripts 1 dependents
jhudsl
ottrpal:Companion Tools for Open-Source Tools for Training Resources (OTTR)
Tools for converting Open-Source Tools for Training Resources (OTTR) courses into Leanpub or Coursera courses. 'ottrpal' is for use with the OTTR Template repository to create courses.
Maintained by Candace Savonen. Last updated 11 days ago.
3 stars 6.50 score 10 scripts 1 dependents
huanglabumn
oncoPredict:Drug Response Modeling and Biomarker Discovery
Allows for building drug response models using screening data between bulk RNA-Seq and a drug response metric and two additional tools for biomarker discovery that have been developed by the Huang Laboratory at University of Minnesota. There are 3 main functions within this package. (1) calcPhenotype is used to build drug response models on RNA-Seq data and impute them on any other RNA-Seq dataset given to the model. (2) GLDS is used to calculate the general level of drug sensitivity, which can improve biomarker discovery. (3) IDWAS can take the results from calcPhenotype and link the imputed response back to available genomic (mutation and CNV alterations) to identify biomarkers. Each of these functions comes from a paper from the Huang research laboratory. Below gives the relevant paper for each function. calcPhenotype - Geeleher et al, Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines. GLDS - Geeleher et al, Cancer biomarker discovery is improved by accounting for variability in general levels of drug sensitivity in pre-clinical models. IDWAS - Geeleher et al, Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies.
Maintained by Robert Gruener. Last updated 12 months ago.
svapreprocesscorestringrbiomartgenefilterorg.hs.eg.dbgenomicfeaturestxdb.hsapiens.ucsc.hg19.knowngenetcgabiolinksbiocgenericsgenomicrangesirangess4vectors
18 stars 6.47 score 41 scripts
selesnow
rgoogleads:Loading Data from 'Google Ads API'
Interface for loading data from 'Google Ads API', see <https://developers.google.com/google-ads/api/docs/start>. Package provide function for authorization and loading reports.
Maintained by Alexey Seleznev. Last updated 3 months ago.
14 stars 6.40 score 15 scripts 1 dependents
atomashevic
transforEmotion:Sentiment Analysis for Text, Image and Video using Transformer Models
Implements sentiment analysis using huggingface <https://huggingface.co> transformer zero-shot classification model pipelines for text and image data. The default text pipeline is Cross-Encoder's DistilRoBERTa <https://huggingface.co/cross-encoder/nli-distilroberta-base> and default image/video pipeline is Open AI's CLIP <https://huggingface.co/openai/clip-vit-base-patch32>. All other zero-shot classification model pipelines can be implemented using their model name from <https://huggingface.co/models?pipeline_tag=zero-shot-classification>.
Maintained by Aleksandar Tomašević. Last updated 3 months ago.
26 stars 6.40 score 12 scripts
thewileylab
ReviewR:A Light-Weight, Portable Tool for Reviewing Individual Patient Records
A portable Shiny tool to explore patient-level electronic health record data and perform chart review in a single integrated framework. This tool supports browsing clinical data in many different formats including multiple versions of the 'OMOP' common data model as well as the 'MIMIC-III' data model. In addition, chart review information is captured and stored securely via the Shiny interface in a 'REDCap' (Research Electronic Data Capture) project using the 'REDCap' API. See the 'ReviewR' website for additional information, documentation, and examples.
Maintained by David Mayer. Last updated 2 years ago.
24 stars 6.33 score 6 scriptsjhudsl
text2speech:Text to Speech Conversion
Converts text into speech using various text-to-speech (TTS) engines and provides an unified interface for accessing their functionality. With this package, users can easily generate audio files of spoken words, phrases, or sentences from plain text data. The package supports multiple TTS engines, including Google's 'Cloud Text-to-Speech API', 'Amazon Polly', Microsoft's 'Cognitive Services Text to Speech REST API', and a free TTS engine called 'Coqui TTS'.
Maintained by Howard Baek. Last updated 2 years ago.
edtech-softwarespeech-synthesistext-to-speechttsvoice
21 stars 6.28 score 9 scripts 2 dependentsusaid-oha-si
gophr:Utility functions related to working with the MER Structured Dataset
This packages contains a number of functions for working with the PEPFAR MSD.
Maintained by Aaron Chafetz. Last updated 5 months ago.
1 stars 6.21 score 182 scripts 1 dependents
njlyon0
supportR:Support Functions for Wrangling and Visualization
Suite of helper functions for data wrangling and visualization. The only theme for these functions is that they tend towards simple, short, and narrowly-scoped. These functions are built for tasks that often recur but are not large enough in scope to warrant an ecosystem of interdependent functions.
Maintained by Nicholas J Lyon. Last updated 4 months ago.
5 stars 6.18 score 15 scripts
nataliepatten
gatoRs:Geographic and Taxonomic Occurrence R-Based Scrubbing
Streamlines downloading and cleaning biodiversity data from Integrated Digitized Biocollections (iDigBio) and the Global Biodiversity Information Facility (GBIF).
Maintained by Natalie N. Patten. Last updated 11 months ago.
11 stars 6.16 score 66 scripts
r-a-dobson
dynamicSDM:Species Distribution and Abundance Modelling at High Spatio-Temporal Resolution
A collection of novel tools for generating species distribution and abundance models (SDM) that are dynamic through both space and time. These highly flexible functions incorporate spatial and temporal aspects across key SDM stages; including when cleaning and filtering species occurrence data, generating pseudo-absence records, assessing and correcting sampling biases and autocorrelation, extracting explanatory variables and projecting distribution patterns. Throughout, functions utilise Google Earth Engine and Google Drive to minimise the computing power and storage demands associated with species distribution modelling at high spatio-temporal resolution.
Maintained by Rachel Dobson. Last updated 1 months ago.
dynamicsdmgoogle-earth-enginegoogledrivesdmspatiotemporalspatiotemporal-data-analysisspatiotemporal-forecastingspecies-distribution-modellingspecies-distributions
6 stars 6.16 score 20 scripts
fhdsl
metricminer:Mine Metrics from Common Places on the Web
Mine metrics on common places on the web through the power of their APIs (application programming interfaces). It also helps make the data in a format that is easily used for a dashboard or other purposes. There is an associated dashboard template and tutorials that are underdevelopment that help you fully utilize 'metricminer'.
Maintained by Candace Savonen. Last updated 6 days ago.
2 stars 6.13 score 21 scripts
eu-ecdc
epitweetr:Early Detection of Public Health Threats from 'Twitter' Data
It allows you to automatically monitor trends of tweets by time, place and topic aiming at detecting public health threats early through the detection of signals (e.g. an unusual increase in the number of tweets). It was designed to focus on infectious diseases, and it can be extended to all hazards or other fields of study by modifying the topics and keywords. More information is available in the 'epitweetr' peer-review publication (doi:10.2807/1560-7917.ES.2022.27.39.2200177).
Maintained by Laura Espinosa. Last updated 1 years ago.
early-warning-systemsepidemic-surveillancelucenemachine-learningsignal-detectionsparktwitter
56 stars 5.98 score 86 scripts
gbganalyst
bulkreadr:The Ultimate Tool for Reading Data in Bulk
Designed to simplify and streamline the process of reading and processing large volumes of data in R, this package offers a collection of functions tailored for bulk data operations. It enables users to efficiently read multiple sheets from Microsoft Excel and Google Sheets workbooks, as well as various CSV files from a directory. The data is returned as organized data frames, facilitating further analysis and manipulation. Ideal for handling extensive data sets or batch processing tasks, bulkreadr empowers users to manage data in bulk effortlessly, saving time and effort in data preparation workflows. Additionally, the package seamlessly works with labelled data from SPSS and Stata.
Maintained by Ezekiel Ogundepo. Last updated 7 months ago.
bulkreadercsv-readerdata-importgooglesheetsmissing-valuesxlsxreader
12 stars 5.94 score 12 scripts
flr
FLBEIA:Bio-Economic Impact Assessment of Management Strategies using FLR
A simulation toolbox that describes a fishery system under a Management Strategy Estrategy approach. The objective of the model is to facilitate the Bio-Economic evaluation of Management strategies. It is multistock, multifleet and seasonal. The simulation is divided in 2 main blocks, the Operating Model (OM) and the Management Procedure (MP). In turn, each of these two blocks is divided in 3 components: the biological, the fleets and the covariables on the one hand, and the observation, the assessment and the advice on the other.
Maintained by FLBEIA Team. Last updated 19 days ago.
11 stars 5.89 score 156 scriptsbioc
miRspongeR:Identification and analysis of miRNA sponge regulation
This package provides several functions to explore miRNA sponge (also called ceRNA or miRNA decoy) regulation from putative miRNA-target interactions or/and transcriptomics data (including bulk, single-cell and spatial gene expression data). It provides eight popular methods for identifying miRNA sponge interactions, and an integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of miRNA sponge modules, and conduct survival analysis of miRNA sponge modules. By using a sample control variable strategy, it provides a function to infer sample-specific miRNA sponge interactions. In terms of sample-specific miRNA sponge interactions, it implements three similarity methods to construct sample-sample correlation network.
Maintained by Junpeng Zhang. Last updated 5 months ago.
geneexpressionbiomedicalinformaticsnetworkenrichmentsurvivalmicroarraysoftwaresinglecellspatialrnaseqcernamirnasponge
5 stars 5.88 score 8 scripts
edhofman
ReSurv:Machine Learning Models For Predicting Claim Counts
Prediction of claim counts using the feature based development factors introduced in the manuscript <doi:10.48550/arXiv.2312.14549>. Implementation of Neural Networks, Extreme Gradient Boosting, and Cox model with splines to optimise the partial log-likelihood of proportional hazard models.
Maintained by Emil Hofman. Last updated 5 months ago.
2 stars 5.87 score 21 scripts
cardiomoon
ggplotAssist:'RStudio' Addin for Teaching and Learning 'ggplot2'
An 'RStudio' addin for teaching and learning making plot using the 'ggplot2' package. You can learn each steps of making plot by clicking your mouse without coding. You can get resultant code for the plot.
Maintained by Keon-Woong Moon. Last updated 7 years ago.
79 stars 5.85 score 18 scripts
richardli
surveyPrev:Mapping the Prevalence of Binary Indicators using Survey Data in Small Areas
Provides a pipeline to perform small area estimation and prevalence mapping of binary indicators using health and demographic survey data, described in Fuglstad et al. (2022) <doi:10.48550/arXiv.2110.09576> and Wakefield et al. (2020) <doi:10.1111/insr.12400>.
Maintained by Qianyu Dong. Last updated 3 days ago.
1 stars 5.76 score 11 scriptsbioc
limpca:An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family of methods
This package has for objectives to provide a method to make Linear Models for high-dimensional designed data. limpca applies a GLM (General Linear Model) version of ASCA and APCA to analyse multivariate sample profiles generated by an experimental design. ASCA/APCA provide powerful visualization tools for multivariate structures in the space of each effect of the statistical model linked to the experimental design and contrarily to MANOVA, it can deal with mutlivariate datasets having more variables than observations. This method can handle unbalanced design.
Maintained by Manon Martin. Last updated 5 months ago.
statisticalmethodprincipalcomponentregressionvisualizationexperimentaldesignmultiplecomparisongeneexpressionmetabolomics
2 stars 5.73 score 2 scriptsbioc
MSstatsLiP:LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.
Maintained by Devon Kohler. Last updated 5 months ago.
immunooncologymassspectrometryproteomicssoftwaredifferentialexpressiononechanneltwochannelnormalizationqualitycontrolcpp
7 stars 5.62 score 5 scriptsbioc
methylclock:Methylclock - DNA methylation-based clocks
This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath's clock, Hannum's clock, BNN, Horvath's skin+blood clock, PedBE clock and Wu's clock. Gestational DNAm age : Knight's clock, Bohlin's clock, Mayne's clock and Lee's clocks. Biological DNAm clocks : Levine's clock and Telomere Length's clock.
Maintained by Dolors Pelegri-Siso. Last updated 5 months ago.
dnamethylationbiologicalquestionpreprocessingstatisticalmethodnormalizationcpp
39 stars 5.52 score 28 scriptsusaid-oha-si
mindthegap:Mind the Gap
Package to tidy UNAIDS estimates (from the EDMS database) as well as plot trends in UNAIDS 95 goals and ART coverage gap by country.
Maintained by Karishma Srikanth. Last updated 3 months ago.
5 stars 5.51 score 13 scriptsropensci
EndoMineR:Functions to mine endoscopic and associated pathology datasets
This script comprises the functions that are used to clean up endoscopic reports and pathology reports as well as many of the scripts used for analysis. The scripts assume the endoscopy and histopathology data set is merged already but it can also be used of course with the unmerged datasets.
Maintained by Sebastian Zeki. Last updated 7 months ago.
endoscopygastroenterologypeer-reviewedsemi-structured-datatext-mining
13 stars 5.47 score 30 scripts
marce10
dynaSpec:Dynamic Spectrogram Visualizations
A set of tools to generate dynamic spectrogram visualizations in video format.
Maintained by Marcelo Araya-Salas. Last updated 1 months ago.
animal-soundsbioacousticsspectrogram
23 stars 5.37 score 34 scripts
andodet
googlePubsubR:R Interface for Google 'Cloud Pub/Sub' REST API
Provides an easy to use interface to the 'Google Pub/Sub' REST API <https://cloud.google.com/pubsub/docs/reference/rest>.
Maintained by Andrea Dodet. Last updated 2 years ago.
10 stars 5.34 score 22 scripts
junjunlab
transPlotR:Visualize Transcript Structures in Elegant Way
To visualize the gene structure with multiple isoforms better, I developed this package to draw different transcript structures easily.
Maintained by Jun Zhang. Last updated 2 years ago.
bedbigwiggenelinkvistranscriptvisualization
73 stars 5.34 score 60 scripts
andrie
mailmerge:Mail Merge Using R Markdown Documents and 'gmailr'
Perform a mail merge (mass email) using the message defined in markdown, the recipients in a 'csv' file, and gmail as the mailing engine. With this package you can parse markdown documents as the body of email, and the 'yaml' header to specify the subject line of the email. Any '{}' braces in the email will be encoded with 'glue::glue()'. You can preview the email in the RStudio viewer pane, and send (draft) email using 'gmailr'.
Maintained by Andrie de Vries. Last updated 1 years ago.
43 stars 5.33 score 10 scripts
nceas
scicomptools:Tools Developed by the NCEAS Scientific Computing Support Team
Set of tools to import, summarize, wrangle, and visualize data. These functions were originally written based on the needs of the various synthesis working groups that were supported by the National Center for Ecological Analysis and Synthesis (NCEAS). These tools are meant to be useful inside and outside of the context for which they were designed.
Maintained by Angel Chen. Last updated 5 months ago.
9 stars 5.26 score 6 scripts
jiang-junyao
CACIMAR:cross-species analysis of cell identities, markers and regulations
A toolkit to perform cross-species analysis based on scRNA-seq data. CACIMAR contains 5 main features. (1) identify Markers in each cluster. (2) Cell type annotaion (3) identify conserved markers. (4) identify conserved cell types. (5) identify conserved modules of regulatory networks.
Maintained by Junyao Jiang. Last updated 4 months ago.
cross-species-analysisscrna-seq
12 stars 5.26 score 6 scripts
usaid-mozambique
sismar:Arrumar dados SISMA
Fornece um conjunto de funções para a criação de conjuntos de dados analíticos a partir de downloads do SISMA e DISA. Inclui funções que arrumam os ficheiros para um formato longo, removem variáveis desnecessárias, e criam colunas úteis para a análise.
Maintained by Joe Lara. Last updated 4 days ago.
2 stars 5.23 score 9 scripts
larsenlab
hlaR:Tools for HLA Data
A streamlined tool for eplet analysis of donor and recipient HLA (human leukocyte antigen) mismatch. Messy, low-resolution HLA typing data is cleaned, and imputed to high-resolution using the NMDP (National Marrow Donor Program) haplotype reference database <https://haplostats.org/haplostats>. High resolution data is analyzed for overall or single antigen eplet mismatch using a reference table (currently supporting 'HLAMatchMaker' <http://www.epitopes.net> versions 2 and 3). Data can enter or exit the workflow at different points depending on the user's aims and initial data quality.
Maintained by Joan Zhang. Last updated 2 years ago.
7 stars 5.15 score 9 scripts
yuanchao-xu
gfer:Green Finance and Environmental Risk
Focuses on data collecting, analyzing and visualization in green finance and environmental risk research and analysis. Main function includes environmental data collecting from official websites such as MEP (Ministry of Environmental Protection of China, <https://www.mee.gov.cn>), water related projects identification and environmental data visualization.
Maintained by Yuanchao Xu. Last updated 12 days ago.
corporate-social-responsibilitycsrdata-analysisdata-scrapingenvironmental-riskgreen-financestock-data
8 stars 5.11 score 16 scripts
jlp-bioinf
rnaCrosslinkOO:Analysis of RNA Crosslinking Data
Analysis of RNA crosslinking data for RNA structure prediction. The package is suitable for the analysis of RNA structure cross-linking data and chemical probing data.
Maintained by Jonathan Price. Last updated 2 months ago.
comradespsoralenrna-crosslinkingrna-structurerna-structure-prediction
1 stars 5.08 score 3 scripts
jobnmadu
Dyn4cast:Dynamic Modeling and Machine Learning Environment
Estimates, predict and forecast dynamic models as well as Machine Learning metrics which assists in model selection for further analysis. The package also have capabilities to provide tools and metrics that are useful in machine learning and modeling. For example, there is quick summary, percent sign, Mallow's Cp tools and others. The ecosystem of this package is analysis of economic data for national development. The package is so far stable and has high reliability and efficiency as well as time-saving.
Maintained by Job Nmadu. Last updated 15 days ago.
data-scienceequal-lenght-forecastforecastingknotsmachine-learningnigeriapredictionregression-modelsspline-modelsstatisticstime-series
4 stars 5.03 score 38 scriptsbioc
MAI:Mechanism-Aware Imputation
A two-step approach to imputing missing data in metabolomics. Step 1 uses a random forest classifier to classify missing values as either Missing Completely at Random/Missing At Random (MCAR/MAR) or Missing Not At Random (MNAR). MCAR/MAR are combined because it is often difficult to distinguish these two missing types in metabolomics data. Step 2 imputes the missing values based on the classified missing mechanisms, using the appropriate imputation algorithms. Imputation algorithms tested and available for MCAR/MAR include Bayesian Principal Component Analysis (BPCA), Multiple Imputation No-Skip K-Nearest Neighbors (Multi_nsKNN), and Random Forest. Imputation algorithms tested and available for MNAR include nsKNN and a single imputation approach for imputation of metabolites where left-censoring is present.
Maintained by Jonathan Dekermanjian. Last updated 5 months ago.
softwaremetabolomicsstatisticalmethodclassificationimputation-methodsmachine-learningmissing-data
2 stars 5.00 score 6 scriptscloudyr
googleCloudVisionR:Access to the 'Google Cloud Vision' API for Image Recognition, OCR and Labeling
Interact with the 'Google Cloud Vision' <https://cloud.google.com/vision/> API in R. Part of the 'cloudyr' <https://cloudyr.github.io/> project.
Maintained by Jeno Pal. Last updated 5 years ago.
7 stars 4.95 score 14 scripts 1 dependents
scholaempirica
reschola:The Schola Empirica Package
A collection of utilies, themes and templates for data analysis at Schola Empirica.
Maintained by Jan Netík. Last updated 6 months ago.
4 stars 4.83 score 14 scripts
nau-ccl
SPARSEMODr:SPAtial Resolution-SEnsitive Models of Outbreak Dynamics
Implementation of spatially-explicit, stochastic disease models with customizable time windows that describe how parameter values fluctuate during outbreaks (e.g., in response to public health or conservation interventions).
Maintained by Joseph Mihaljevic. Last updated 3 years ago.
1 stars 4.78 score 8 scripts
diogoferrari
hdpGLM:Hierarchical Dirichlet Process Generalized Linear Models
Implementation of MCMC algorithms to estimate the Hierarchical Dirichlet Process Generalized Linear Model (hdpGLM) presented in the paper Ferrari (2020) Modeling Context-Dependent Latent Heterogeneity, Political Analysis <DOI:10.1017/pan.2019.13> and <doi:10.18637/jss.v107.i10>.
Maintained by Diogo Ferrari. Last updated 1 years ago.
dirichlet-process-mixtureshierarchical-clusteringnonparametricnonparametricbayesnpbsemi-parametricopenblascpp
12 stars 4.78 score 5 scriptscardiomoon
dplyrAssist:RStudio Addin for Teaching and Learning Data Manipulation Using 'dplyr'
An RStudio addin for teaching and learning data manipulation using the 'dplyr' package. You can learn each steps of data manipulation by clicking your mouse without coding. You can get resultant data (as a 'tibble') and the code for data manipulation.
Maintained by Keon-Woong Moon. Last updated 7 years ago.
12 stars 4.78 score 7 scripts
mkorvink
archetyper:An Archetype for Data Mining and Data Science Projects
A project template to support the data science workflow.
Maintained by Michael Korvink. Last updated 4 years ago.
6 stars 4.78 score 7 scripts
lter
ltertools:Tools Developed by the Long Term Ecological Research Community
Set of the data science tools created by various members of the Long Term Ecological Research (LTER) community. These functions were initially written largely as standalone operations and have later been aggregated into this package.
Maintained by Nicholas Lyon. Last updated 4 days ago.
3 stars 4.78 score 4 scriptsbioc
Polytect:An R package for digital data clustering
Polytect is an advanced computational tool designed for the analysis of multi-color digital PCR data. It provides automatic clustering and labeling of partitions into distinct groups based on clusters first identified by the flowPeaks algorithm. Polytect is particularly useful for researchers in molecular biology and bioinformatics, enabling them to gain deeper insights into their experimental results through precise partition classification and data visualization.
Maintained by Yao Chen. Last updated 3 months ago.
ddpcrclusteringmultichannelclassification
4.74 score 4 scriptsbioc
GNOSIS:Genomics explorer using statistical and survival analysis in R
GNOSIS incorporates a range of R packages enabling users to efficiently explore and visualise clinical and genomic data obtained from cBioPortal. GNOSIS uses an intuitive GUI and multiple tab panels supporting a range of functionalities. These include data upload and initial exploration, data recoding and subsetting, multiple visualisations, survival analysis, statistical analysis and mutation analysis, in addition to facilitating reproducible research.
Maintained by Lydia King. Last updated 5 months ago.
5 stars 4.70 score 2 scripts
osimon81
SqueakR:An Experiment Interface for 'DeepSqueak' Bioacoustics Research
Data processing and visualizations for rodent vocalizations exported from 'DeepSqueak'. These functions are compatible with the 'SqueakR' Shiny Dashboard, which can be used to visualize experimental results and analyses.
Maintained by Simon Ogundare. Last updated 3 years ago.
9 stars 4.65 score 5 scriptsbioc
dce:Pathway Enrichment Based on Differential Causal Effects
Compute differential causal effects (dce) on (biological) networks. Given observational samples from a control experiment and non-control (e.g., cancer) for two genes A and B, we can compute differential causal effects with a (generalized) linear regression. If the causal effect of gene A on gene B in the control samples is different from the causal effect in the non-control samples the dce will differ from zero. We regularize the dce computation by the inclusion of prior network information from pathway databases such as KEGG.
Maintained by Kim Philipp Jablonski. Last updated 3 months ago.
softwarestatisticalmethodgraphandnetworkregressiongeneexpressiondifferentialexpressionnetworkenrichmentnetworkkeggbioconductorcausality
13 stars 4.59 score 4 scripts
mariallr
amanida:Meta-Analysis for Non-Integral Data
Combination of results for meta-analysis using significance and effect size only. P-values and fold-change are combined to obtain a global significance on each metabolite. Produces a volcano plot summarising the relevant results from meta-analysis. Vote-counting reports for metabolites. And explore plot to detect discrepancies between studies at a first glance. Methodology is described in the Llambrich et al. (2021) <doi:10.1093/bioinformatics/btab591>.
Maintained by Maria Llambrich. Last updated 1 years ago.
7 stars 4.54 score 7 scripts
thinkr-open
tutor:Deploy shiny_prerendered Rmds
Deploy Rmd using shiny_prerendered.
Maintained by vincent guyader. Last updated 10 months ago.
4 stars 4.51 score 102 scripts
mbannick
RobinCar:Robust Inference for Covariate Adjustment in Randomized Clinical Trials
Performs robust estimation and inference when using covariate adjustment and/or covariate-adaptive randomization in randomized clinical trials. Ting Ye, Jun Shao, Yanyao Yi, Qinyuan Zhao (2023) <doi:10.1080/01621459.2022.2049278>. Ting Ye, Marlena Bannick, Yanyao Yi, Jun Shao (2023) <doi:10.1080/24754269.2023.2205802>. Ting Ye, Jun Shao, Yanyao Yi (2023) <doi:10.1093/biomet/asad045>. Marlena Bannick, Jun Shao, Jingyi Liu, Yu Du, Yanyao Yi, Ting Ye (2024) <doi:10.48550/arXiv.2306.10213>.
Maintained by Marlena Bannick. Last updated 21 days ago.
6 stars 4.42 score 11 scripts
annechao
MF.beta4:Measuring Ecosystem Multi-Functionality and Its Decomposition
Provide simple functions to (i) compute a class of multi-functionality measures for a single ecosystem for given function weights, (ii) decompose gamma multi-functionality for pairs of ecosystems and K ecosystems (K can be greater than 2) into a within-ecosystem component (alpha multi-functionality) and an among-ecosystem component (beta multi-functionality). In each case, the correlation between functions can be corrected for. Based on biodiversity and ecosystem function data, this software also facilitates graphics for assessing biodiversity-ecosystem functioning relationships across scales.
Maintained by Anne Chao. Last updated 4 months ago.
4.40 score 3 scripts
wenlong-liu
usfertilizer:County-Level Estimates of Fertilizer Application in USA
Compiled and cleaned the county-level estimates of fertilizer, nitrogen and phosphorus, from 1945 to 2012 in United States of America (USA). The commercial fertilizer data were originally generated by USGS based on the sales data of commercial fertilizer. The manure data were estimated based on county-level population data of livestock, poultry, and other animals. See the user manual for detailed data sources and cleaning methods. 'usfertilizer' utilized the tidyverse to clean the original data and provide user-friendly dataframe. Please note that USGS does not endorse this package. Also data from 1986 is not available for now.
Maintained by Wenlong Liu. Last updated 7 years ago.
11 stars 4.34 score 1 scripts
g6t
cloudfs:Streamlined Interface to Interact with Cloud Storage Platforms
A unified interface for simplifying cloud storage interactions, including uploading, downloading, reading, and writing files, with functions for both 'Google Drive' (<https://www.google.com/drive/>) and 'Amazon S3' (<https://aws.amazon.com/s3/>).
Maintained by Iaroslav Domin. Last updated 11 months ago.
2 stars 4.30 score 3 scriptsbioc
AnVILBilling:Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org).
AnVILBilling helps monitor AnVIL-related costs in R, using queries to a BigQuery table to which costs are exported daily. Functions are defined to help categorize tasks and associated expenditures, and to visualize and explore expense profiles over time. This package will be expanded to help users estimate costs for specific task sets.
Maintained by Vince Carey. Last updated 5 months ago.
4.30 score 5 scripts
gongcastro
bvq:Barcelona Vocabulary Questionnaire Database and Helper Functions
Download, clean, and process the Barcelona Vocabulary Questionnaire (BVQ) data. BVQ is a vocabulary inventory developed for assesing the vocabulary of Catalan-Spanish bilinguals infants from the Metropolitan Area of Barcelona (Spain). This package includes functions to download the data from formr servers, and return the processed data in multiple formats.
Maintained by Gonzalo Garcia-Castro. Last updated 3 months ago.
bilingualismlanguagepsycholinguisticsvocabulary
1 stars 4.26 score 8 scripts
kiangkiangkiang
ggESDA:Exploratory Symbolic Data Analysis with 'ggplot2'
Implements an extension of 'ggplot2' and visualizes the symbolic data with multiple plot which can be adjusted by more general and flexible input arguments. It also provides a function to transform the classical data to symbolic data by both clustering algorithm and customized method.
Maintained by Bo-Syue Jiang. Last updated 2 years ago.
21 stars 4.02 score 9 scripts
bahlolab
UKB.COVID19:UK Biobank COVID-19 Data Processing and Risk Factor Association Tests
Process UK Biobank COVID-19 test result data for susceptibility, severity and mortality analyses, perform potential non-genetic COVID-19 risk factor and co-morbidity association tests. Wang et al. (2021) <doi:10.5281/zenodo.5174381>.
Maintained by Longfei Wang. Last updated 8 months ago.
1 stars 4.00 score 4 scriptsbioc
SARC:Statistical Analysis of Regions with CNVs
Imports a cov/coverage file (normalised read coverages from BAM files) and a cnv file (list of CNVs - similiar to a BED file) from WES/ WGS CNV (copy number variation) detection pipelines and utilises several metrics to weigh the likelihood of a sample containing a detected CNV being a true CNV or a false positive. Highly useful for diagnostic testing to filter out false positives to provide clinicians with fewer variants to interpret. SARC uniquely only used cov and csv (similiar to BED file) files which are the common CNV pipeline calling filetypes, and can be used as to supplement the Interactive Genome Browser (IGV) to generate many figures automatedly, which can be especially helpful in large cohorts with 100s-1000s of patients.
Maintained by Krutik Patel. Last updated 5 months ago.
softwarecopynumbervariationvisualizationdnaseqsequencing
4.00 score 2 scriptsusaid-oha-si
selfdestructin5:Creates SI OHA Mission Director Briefers
Creates a series of data frames that can be passed to a gt() to create the PEPFAR summary tables.
Maintained by Tim Essam. Last updated 1 months ago.
1 stars 3.98 score 21 scripts
exetrujillo
datamedios:Scraping Chilean Media
A system for extracting news from Chilean media, specifically through Web Scapping from Chilean media. The package allows for news searches using search phrases and date filters, and returns the results in a structured format, ready for analysis. Additionally, it includes functions to clean the extracted data, visualize it, and store it in databases. All of this can be done automatically, facilitating the collection and analysis of relevant information from Chilean media.
Maintained by Exequiel Trujillo. Last updated 1 months ago.
2 stars 3.90 score
alexchristensen
latentFactoR:Data Simulation Based on Latent Factors
Generates data based on latent factor models. Data can be continuous, polytomous, dichotomous, or mixed. Skews, cross-loadings, wording effects, population errors, and local dependencies can be added. All parameters can be manipulated. Data categorization is based on Garrido, Abad, and Ponsoda (2011) <doi:10.1177/0013164410389489>.
Maintained by Alexander Christensen. Last updated 8 months ago.
3 stars 3.88 score 2 scripts
eurostat
correspondenceTables:Creating Correspondence Tables Between Two Statistical Classifications
A candidate correspondence table between two classifications can be created when there are correspondence tables leading from the first classification to the second one via intermediate 'pivot' classifications. The correspondence table between two statistical classifications can be updated when one of the classifications gets updated to a new version.
Maintained by Mátyás Mészáros. Last updated 2 months ago.
eurostatstatistical-classification
7 stars 3.85 score 4 scripts
malfly
JAGStree:Automatically Write 'JAGS' Code for Hierarchical Bayesian Models on Trees
When relationships between sources of data can be represented by a tree, the generation of appropriate Markov Chain Monte Carlo modeling code to be used with 'JAGS' to run a Bayesian hierarchical model can be automatically generated by this package. Any admissible tree-structured data can be used, under the assumption that node counts are multinomial and branching probabilities are Dirichlet among sibling groups. The methodological basis used to create this package can be found in Flynn (2023) <http://hdl.handle.net/2429/86174>.
Maintained by Mallory J Flynn. Last updated 5 months ago.
3.70 score
syneoshealth
puzzle:Assembling Data Sets for Non-Linear Mixed Effects Modeling
To Simplify the time consuming and error prone task of assembling complex data sets for non-linear mixed effects modeling. Users are able to select from different absorption processes such as zero and first order, or a combination of both. Furthermore, data sets containing data from several entities, responses, and covariates can be simultaneously assembled.
Maintained by Mario Gonzalez Sales. Last updated 5 years ago.
3 stars 3.65 score 9 scripts
celevitz
touRnamentofchampions:Tournament of Champions Data
Several datasets which describe the challenges and results of competitions in Tournament of Champions. This data is useful for practicing data wrangling, graphing, and analyzing how each season of Tournament of Champions played out.
Maintained by Levitz Carly. Last updated 2 days ago.
3.60 score
melodyaowen
crt2power:Designing Cluster-Randomized Trials with Two Continuous Co-Primary Outcomes
Provides methods for powering cluster-randomized trials with two continuous co-primary outcomes using five key design techniques. Includes functions for calculating required sample size and statistical power. For more details on methodology, see Owen et al. (2025) <doi:10.1002/sim.70015>, Yang et al. (2022) <doi:10.1111/biom.13692>, Pocock et al. (1987) <doi:10.2307/2531989>, Vickerstaff et al. (2019) <doi:10.1186/s12874-019-0754-4>, and Li et al. (2020) <doi:10.1111/biom.13212>.
Maintained by Melody Owen. Last updated 18 days ago.
3.60 score 2 scripts
aviralvijay-gslab
nonet:Weighted Average Ensemble without Training Labels
It provides ensemble capabilities to supervised and unsupervised learning models predictions without using training labels. It decides the relative weights of the different models predictions by using best models predictions as response variable and rest of the mo. User can decide the best model, therefore, It provides freedom to user to ensemble models based on their design solutions.
Maintained by Aviral Vijay. Last updated 6 years ago.
1 stars 3.41 score 17 scriptsropensci
ReLTER:An Interface for the eLTER Community
ReLTER provides access to DEIMS-SDR (https://deims.org/), and allows interaction with data and software implemented by eLTER Research Infrastructure (RI) thus improving data sharing among European LTER projects. ReLTER uses the R language to access and interact with the DEIMS-SDR archive of information shared by the Long Term Ecological Research (LTER) network. This package grew within eLTER H2020 as a major project that will help advance the development of European Long-Term Ecosystem Research Infrastructures (eLTER RI - https://elter-ri.eu). The ReLTER package functions in particular allow to: - retrieve the information about entities (e.g. sites, datasets, and activities) shared by DEIMS-SDR (see e.g. get_site_info function); - interact with the [ODSEurope](maps.opendatascience.eu) starting with the dataset shared by [DEIMS-SDR](https://deims.org/) (see e.g. [get_site_ODS](https://docs.ropensci.org/ReLTER/reference/get_site_ODS.html) function); - use the eLTER site informations to download and crop geospatial data from other platforms (see e.g. get_site_ODS function); - improve the quality of the dataset (see e.g. get_id_worms). Functions currently implemented are derived from discussions of the needs among the eLTER users community. The ReLTER package will continue to follow the progress of eLTER-RI and evolve, adding new tools and improvements as required.
Maintained by Alessandro Oggioni. Last updated 1 years ago.
biodiversity-informaticsdata-scienceecologyelterresearch-infrastructure
12 stars 3.38 score 4 scriptsropensci
quartificate:Transform Google Docs into Quarto Books
Automate the Transformation of a Google Document into a Quarto Book source.
Maintained by Maëlle Salmon. Last updated 2 months ago.
48 stars 3.38 score
blaserlab
datascience.curriculum:Data Science 2023
What the package does (one paragraph).
Maintained by Brad Blaser. Last updated 2 years ago.
1 stars 3.30 score 8 scripts
notplancha
settingsSync:'Rstudio' Addin to Sync Settings and Keymaps
Provides a 'Rstudio' addin to download, merge and upload 'Rstudio' settings and keymaps, essentially 'syncing them' at will. It uses 'Google Drive' as a cloud storage to keep the settings and keymaps files.
Maintained by André Plancha. Last updated 10 months ago.
google-driverstudiorstudio-addin
2 stars 3.30 score
jiajingz
CopSens:Copula-Based Sensitivity Analysis for Observational Causal Inference
Implements the copula-based sensitivity analysis method, as discussed in Copula-based Sensitivity Analysis for Multi-Treatment Causal Inference with Unobserved Confounding <arXiv:2102.09412>, with Gaussian copula adopted in particular.
Maintained by Jiajing Zheng. Last updated 2 years ago.
4 stars 3.30 score 7 scripts
predictiveecology
SpaDES.experiment:Simulation Experiments Within The SpaDES Ecosystem
Tools to do simulation experiments within the SpaDES ecosystem. This includes replication, parameter sweeps, scenario analysis, pattern oriented modeling, and simulation experiments. The package introduces a new object class, the simLists, which is an environment that contains many simList class objects. This package also includes tools to do post hoc analyses of such simLists objects.
Maintained by Eliot J B McIntire. Last updated 4 months ago.
1 stars 3.30 score 2 scripts
mingshi1
LipidomicsR:Elegant Tools for Processing and Visualization of Lipidomics Data
An elegant tool for processing and visualizing lipidomics data generated by mass spectrometry. 'LipidomicsR' simplifies channel and replicate handling while providing thorough lipid species annotation. Its visualization capabilities encompass principal components analysis plots, heatmaps, volcano plots, and radar plots, enabling concise data summarization and quality assessment. Additionally, it can generate bar plots and line plots to visualize the abundance of each lipid species.
Maintained by Hengyu Zhu. Last updated 11 months ago.
3.30 score 1 scripts
impaug
UpAndDownPlots:Displays Percentage and Absolute Changes
Displays percentage changes by height and absolute changes by area for up to three nested or non-nested levels. The plots visualise changes in indices and markets, showing how the changes for sectors or for individual components contribute to the overall change. Data can be classified by up to three levels of grouping variables in a layered, hierarchical plot. Each level can be ordered in several ways including by baseline, by percentage change, and by absolute change. The vignettes give examples.
Maintained by Antony Unwin. Last updated 12 months ago.
3.30 score 6 scripts
jgeller112
webgazeR:Tools for Processing Webcam Eye Tracking Data
A companion package to gazeR. Functions for reading and pre-processing webcam eye tracking data.
Maintained by Jason Geller. Last updated 5 days ago.
1 stars 3.25 score 21 scripts
ku-awdc
EpiLinx:Interactive Visualization Tool for Nosocomial Outbreaks
What the package does (one paragraph).
Maintained by Anna Emilie Henius. Last updated 2 months ago.
3.18 score
coreofscience
margaret:Scientometric Analysis Minciencias
The target of 'margaret' is help to extract data from Minciencias to analyze scientific production in Colombia.
Maintained by Bryan Arias. Last updated 2 years ago.
3 stars 3.18 score 4 scripts
dobrowski
MCOE:Creates New Folders and Loads Standard Practices for Monterey County Office of Education
Basic Setup for Projects in R for Monterey County Office of Education. It contains functions often used in the analysis of education data in the county office including seeing if an item is not in a list, rounding in the manner the general public expects, including logos for districts, switching between district names and their county-district-school codes, accessing the local 'SQL' table and making thematically consistent graphs.
Maintained by David Dobrowski. Last updated 1 years ago.
1 stars 3.11 score 26 scripts
ropengov
europarl:Scrap Data from Europarlament's Website
Scrap data from europarlament's website.
Maintained by The package maintainer. Last updated 2 years ago.
11 stars 3.04 scoreusaid-oha-si
themask:Masks and houses the PEPFAR MSD-style training dataset for testing and training
This package creates and hosts a masked, dummy dataset that should be used for testing, training, and demoing instead of using actual PEPFAR data.
Maintained by Aaron Chafetz. Last updated 10 months ago.
1 stars 3.00 score 8 scripts
gefeizhang
statVisual:Statistical Visualization Tools
Visualization functions in the applications of translational medicine (TM) and biomarker (BM) development to compare groups by statistically visualizing data and/or results of analyses, such as visualizing data by displaying in one figure different groups' histograms, boxplots, densities, scatter plots, error-bar plots, or trajectory plots, by displaying scatter plots of top principal components or dendrograms with data points colored based on group information, or visualizing volcano plots to check the results of whole genome analyses for gene differential expression.
Maintained by Wenfei Zhang. Last updated 5 years ago.
3.00 score 3 scripts
kevinegan31
ARGOS:Automatic Regression for Governing Equations (ARGOS)
Comprehensive set of tools for performing system identification of both linear and nonlinear dynamical systems directly from data. The Automatic Regression for Governing Equations (ARGOS) simplifies the complex task of constructing mathematical models of dynamical systems from observed input and output data, supporting various types of systems, including those described by ordinary differential equations. It employs optimal numerical derivatives for enhanced accuracy and employs formal variable selection techniques to help identify the most relevant variables, thereby enabling the development of predictive models for system behavior analysis.
Maintained by Kevin Egan. Last updated 1 years ago.
2 stars 3.00 score 3 scripts
markheckmann
OpenRepGrid.ic:Interpretive Clustering for Repertory Grids
Shiny UI to identify cliques of related constructs in repertory grid data. See Burr, King, & Heckmann (2020) <doi:10.1080/14780887.2020.1794088> for a description of the interpretive clustering (IC) method.
Maintained by Mark Heckmann. Last updated 1 years ago.
clusteringconstructsgridrepertoryrepgridshiny
2 stars 3.00 score 8 scripts
igrave
ladder:Get on to the Slides
Create tables from within R directly on Google Slides presentations. Currently supports matrix, data.frame and 'flextable' objects.
Maintained by Isaac Gravestock. Last updated 16 days ago.
1 stars 2.93 score 3 scripts
myaseen208
baystability:Bayesian Stability Analysis of Genotype by Environment Interaction (GEI)
Performs general Bayesian estimation method of linear–bilinear models for genotype × environment interaction. The method is explained in Perez-Elizalde, S., Jarquin, D., and Crossa, J. (2011) (<doi:10.1007/s13253-011-0063-9>).
Maintained by Muhammad Yaseen. Last updated 6 months ago.
2.81 score 13 scriptsselesnow
rytstat:Work with 'YouTube API'
Provide function for get data from 'YouTube Data API' <https://developers.google.com/youtube/v3/docs/>, 'YouTube Analytics API' <https://developers.google.com/youtube/analytics/reference/> and 'YouTube Reporting API' <https://developers.google.com/youtube/reporting/v1/reports>.
Maintained by Alexey Seleznev. Last updated 10 months ago.
1 stars 2.78 score 12 scripts
pedrocava
basedosdados:'Base Dos Dados' R Client
An R interface to the 'Base dos Dados' API <https:basedosdados.github.io/mais/py_reference_api/>). Authenticate your project, query our tables, save data to disk and memory, all from R.
Maintained by Pedro Cavalcante. Last updated 2 years ago.
2.70 score 101 scripts
oyshilin
Sysrecon:Systematical Metabolic Reconstruction
In the past decade, genome-scale metabolic reconstructions have widely been used to comprehend the systems biology of metabolic pathways within an organism. Different GSMs are constructed using various techniques that require distinct steps, but the input data, information conversion and software tools are neither concisely defined nor mathematically or programmatically formulated in a context-specific manner.The tool that quantitatively and qualitatively specifies each reconstruction steps and can generate a template list of reconstruction steps dynamically selected from a reconstruction step reservoir, constructed based on all available published papers.
Maintained by Shilin Ouyang. Last updated 2 years ago.
2.70 score 1 scripts
cran
PEIMAN2:Post-Translational Modification Enrichment, Integration, and Matching Analysis
Functions and mined database from 'UniProt' focusing on post-translational modifications to do single enrichment analysis (SEA) and protein set enrichment analysis (PSEA). Payman Nickchi, Mehdi Mirzaie, Marc Baumann, Amir Ata Saei, Mohieddin Jafari (2022) <bioRxiv:10.1101/2022.11.09.515610>.
Maintained by Payman Nickchi. Last updated 2 years ago.
2.70 score
sumanstats
phrases:Phrasal Verbs in English Club Website
Contains all phrasal verbs listed in <https://www.englishclub.com/ref/Phrasal_Verbs/> as data frame. Useful for educational purpose as well as for text mining.
Maintained by Suman Khanal. Last updated 2 years ago.
1 stars 2.70 score 4 scripts
egonzato
windows.pls:Segmentation Approaches in Chemometrics
Evaluation of prediction performance of smaller regions of spectra for Chemometrics. Segmentation of spectra, evolving dimensions regions and sliding windows as selection methods. Election of the best model among those computed based on error metrics. Chen et al.(2017) <doi:10.1007/s00216-017-0218-9>.
Maintained by Elia Gonzato. Last updated 2 years ago.
2.70 score 4 scriptscran
CSCNet:Fitting and Tuning Regularized Cause-Specific Cox Models with Elastic-Net Penalty
Flexible tools to fit, tune and obtain absolute risk predictions from regularized cause-specific cox models with elastic-net penalty.
Maintained by Shahin Roshani. Last updated 2 years ago.
2.70 score
giocomai
rbackupr:An R package to backup folders to Google Drive with limited permissions
Backup files and folders to Google Drive without giving access to all of your drive.
Maintained by Giorgio Comai. Last updated 1 years ago.
1 stars 2.70 score
mubarakfadhlul
hosm:High Order Spatial Matrix
Automatically displays the order and spatial weighting matrix of the distance between locations. This concept was derived from the research of Mubarak, Aslanargun, and Siklar (2021) <doi:10.52403/ijrr.20211150> and Mubarak, Aslanargun, and Siklar (2022) <doi:10.17654/0972361722052>. Distance data between locations can be imported from 'Ms. Excel', 'maps' package or created in 'R' programming directly. This package also provides 5 simulations of distances between locations derived from fictitious data, the 'maps' package, and from research by Mubarak, Aslanargun, and Siklar (2022) <doi:10.29244/ijsa.v6i1p90-100>.
Maintained by Fadhlul Mubarak. Last updated 2 years ago.
2.70 score
xuechan-li
DYNATE:Dynamic Aggregation Testing
A multiple testing procedure aims to find the rare-variant association regions. When variants are rare, the single variant association test approach suffers from low power. To improve testing power, the procedure dynamically and hierarchically aggregates smaller genome regions to larger ones and performs multiple testing for disease associations with a controlled node-level false discovery rate. This method are members of the family of ancillary information assisted recursive testing introduced in Pura, Li, Chan and Xie (2021) <arXiv:1906.07757v2> and Li, Sung and Xie (2021) <arXiv:2103.11085v2>.
Maintained by Xuechan Li. Last updated 2 years ago.
2.70 score 6 scripts
byzheng
expDB:Database for Experiment Dataset
A 'SQLite' database is designed to store all information of experiment-based data including metadata, experiment design, managements, phenotypic values and climate records. The dataset can be imported from an 'Excel' file.
Maintained by Bangyou Zheng. Last updated 1 years ago.
2.70 score 4 scripts
mohmedsoudy
ORTSC:Connects to Google Cloud API for Label Detection
Connects to Google cloud vision <https://cloud.google.com/vision> to perform label detection and repurpose this feature for image classification.
Maintained by Mohamed Soudy. Last updated 4 years ago.
1 stars 2.70 score
bsnatr
tswge:Time Series for Data Science
Accompanies the texts Time Series for Data Science with R by Woodward, Sadler and Robertson & Applied Time Series Analysis with R, 2nd edition by Woodward, Gray, and Elliott. It is helpful for data analysis and for time series instruction.
Maintained by Bivin Sadler. Last updated 2 years ago.
2.70 score 496 scriptsgiocomai
cornucopia:A cornucopia is like a funnel that keeps on giving
Facilitate reporting on sponsored and organic activities on Facebook, Instagram, and LinkedIn (currently), estimate and visualise the result of marketing funnels (long term)
Maintained by Giorgio Comai. Last updated 4 days ago.
facebookfacebook-apifacebook-graph-apiinstagraminstagram-apilinkedinmarketing-api
2.65 score
cct-datascience
datadrivencv:Templates and helper functions for building a CV with spreadsheets
Separates the CV format from the content using spreadsheets, RMarkdown, and Pagedown. Built to allow easy out-of-the-box behavior, but also to allow you to go beyond the defaults with customization and lack of lock-in to a given format.
Maintained by Nick Strayer. Last updated 1 years ago.
2.59 score 39 scripts
pifsc-protected-species-division
crputils:Miscellaneous R Utilities Useful to CRP
A collection of miscellaneous utilities that are useful for various research activities conducted by the Cetacean Research Program (CRP) at NOAA NMFS Pacific Islands Fisheries Science Center. This includes utilities for working with latitude and longitude data, gpx file creation, and more to come.
Maintained by Selene Fregosi. Last updated 5 days ago.
1 stars 2.54 score 1 scripts
jingyiliang1009
ShapleyValue:Shapley Value Regression for Relative Importance of Attributes
Shapley Value Regression for calculating the relative importance of independent variables in linear regression with avoiding the collinearity.
Maintained by Jingyi Liang. Last updated 4 years ago.
2.48 score 10 scripts 1 dependents
stephenturner
Tverse:Meta package that installs my most commonly used packages
Meta package that installs my most commonly used packages.
Maintained by Stephen Turner. Last updated 7 months ago.
6 stars 2.48 score
inventionate
TimeSpaceAnalysis:Statistical tools for time-space analysis
Use Geometric Data Analysis approaches (e.g. MCA or MFA), time pattern analysis (see "time sequence clustering") and places chronologies (see "time geography") analysis.
Maintained by Fabian Mundt. Last updated 22 days ago.
2.48 score 2 scriptsigrave
ladder.api:Google Slides API client and tools
Create, read and modify Slides presentations with full REST API functionality.
Maintained by Isaac Gravestock. Last updated 8 months ago.
2.40 score
drmowinckels
tidyquintro:Quick Intro to Tidyverse
A 4 hour workshop with quick introduction to tidyverse.
Maintained by Athanasia Mo Mowinckel. Last updated 2 years ago.
3 stars 2.38 score 16 scripts
emptyfield-ds
quarto.workshop:Install Materials for Reproducible Research in R with Quarto
Install learning materials for Reproducible Research in R with Quarto.
Maintained by Malcolm Barrett. Last updated 2 years ago.
4 stars 2.30 score
vharntzen
doublIn:Estimate Incubation or Latency Time using Doubly Interval Censored Observations
Visualize contact tracing data using a 'shiny' app and estimate the incubation or latency time of an infectious disease respecting the following characteristics in the analysis; (i) doubly interval censoring with (partly) overlapping or distinct windows; (ii) an infection risk corresponding to exponential growth; (iii) right truncation allowing for individual truncation times; (iv) different choices concerning the family of the distribution. For our earlier work, we refer to Arntzen et al. (2023) <doi:10.1002/sim.9726>. A paper describing our approach in detail will follow.
Maintained by Vera Arntzen. Last updated 10 months ago.
2.30 score 3 scripts
rdinnager
sdmpack:FIU SDM Course Package
Course material for FIU course on SDM
Maintained by Russell Dinnage. Last updated 1 years ago.
2.08 score 24 scriptsusaid-oha-si
COVIDutilities:Pulls and Returns Tidy COVID-19 Data
What the package does (one paragraph).
Maintained by Tim Essam. Last updated 3 years ago.
2.06 score 23 scripts
drphilippedb
div:Report on Diversity and Inclusion in a Corporate Setting
Facilitate the analysis of teams in a corporate setting: assess the diversity per grade and job, present the results, search for bias (in hiring and/or promoting processes). It also provides methods to simulate the effect of bias, random team-data, etc. White paper: 'Philippe J.S. De Brouwer' (2021) <http://www.de-brouwer.com/assets/div/div-white-paper.pdf>. Book (chapter 36): 'Philippe J.S. De Brouwer' (2020, ISBN:978-1-119-63272-6) and 'Philippe J.S. De Brouwer' (2020) <doi:10.1002/9781119632757>.
Maintained by Philippe J.S. De Brouwer. Last updated 4 years ago.
2.05 score 16 scripts
foocheung
dumbbell:Displaying Changes Between Two Points Using Dumbbell Plots
Creates a Dumbbell Plot.
Maintained by Foo Cheung. Last updated 4 years ago.
2.00 score 9 scripts
matt-dray
tidyquiz:A Tidyverse Quiz
The package contains a multiple-choice quiz built with {learnr} to test your knowledge of the functions of the tidyverse.
Maintained by Matt Dray. Last updated 4 years ago.
2 stars 2.00 score 7 scripts
cran
RanglaPunjab:Displays Palette of 5 Colors
Displays palette of 5 colors based on photos depicting the unique and vibrant culture of Punjab in Northern India. Since Punjab translates to ``Land of 5 Rivers'' there are 5 colors per palette. If users need more than 5 colors, they can merge 2 to 3 palettes to create their own color-combination, or they can cherry-pick their own custom colors. Users can view up to 3 palettes together. Users can also list all the palette choices. And last but not least, users can see the photo that inspired a particular palette.
Maintained by Sonia Ahluwalia. Last updated 7 years ago.
2.00 score
yizhuo-wang
CondiS:Censored Data Imputation for Direct Modeling
Impute the survival times for censored observations based on their conditional survival distributions derived from the Kaplan-Meier estimator. 'CondiS' can replace the censored observations with the best approximations from the statistical model, allowing for direct application of machine learning-based methods. When covariates are available, 'CondiS' is extended by incorporating the covariate information through machine learning-based regression modeling ('CondiS_X'), which can further improve the imputed survival time.
Maintained by Yizhuo Wang. Last updated 3 years ago.
2.00 score 3 scripts
euctrl-pru
HexAeroR:A package to determine used airports, runways, taxiways and stands based on available flight coordinates.
HexAeroR is a EUROCONTROL R package designed for aviation professionals and data analysts. It allows for the determination of used airports, runways, taxiways, and stands based on available (ADS-B) flight trajectory coordinates. This tool aims to enhance aviation data analysis, facilitating the extraction of milestones for performance analysis.
Maintained by Quinten Goens. Last updated 1 years ago.
adepadesaircraftairportaprondetectioneurocontrolh3hexaerohexaerorrunwaystandstaxiwaystrajectoryuber
2.00 score 2 scripts
gloewing
studyStrap:Study Strap and Multi-Study Learning Algorithms
Implements multi-study learning algorithms such as merging, the study-specific ensemble (trained-on-observed-studies ensemble) the study strap, the covariate-matched study strap, covariate-profile similarity weighting, and stacking weights. Embedded within the 'caret' framework, this package allows for a wide range of single-study learners (e.g., neural networks, lasso, random forests). The package offers over 20 default similarity measures and allows for specification of custom similarity measures for covariate-profile similarity weighting and an accept/reject step. This implements methods described in Loewinger, Kishida, Patil, and Parmigiani. (2019) <doi:10.1101/856385>.
Maintained by Gabriel Loewinger. Last updated 5 years ago.
2.00 score 2 scripts
aaronmilloro
metaprotr:Metaproteomics Post-Processing Analysis
Set of tools for descriptive analysis of metaproteomics data generated from high-throughput mass spectrometry instruments. These tools allow to cluster peptides and proteins abundance, expressed as spectral counts, and to manipulate them in groups of metaproteins. This information can be represented using multiple visualization functions to portray the global metaproteome landscape and to differentiate samples or conditions, in terms of abundance of metaproteins, taxonomic levels and/or functional annotation. The provided tools allow to implement flexible analytical pipelines that can be easily applied to studies interested in metaproteomics analysis.
Maintained by Aaron Millan-Oropeza. Last updated 4 years ago.
2 stars 2.00 scorecran
googleTagManageR:Access the 'Google Tag Manager' API using R
Interact with the 'Google Tag Manager' API <https://developers.google.com/tag-platform/tag-manager/api/v2>, enabling scripted deployments and updates across multiple tags, triggers, variables and containers.
Maintained by James Cottrill. Last updated 3 years ago.
1.70 score
panukatan
openbangsamoro:An Interface to the OpenBangsamoro Database
The OpenBangsamoro initiative supports the use of open statistical, geospatial, and administrative data for transparent, accountable, and participatory decision-making as the Autonomous Region in Muslim Mindanao (ARMM) transforms into the Bangsamoro Autonomous Region in Muslim Mindanao.
Maintained by Ernest Guevarra. Last updated 1 years ago.
1 stars 1.70 score
katilingban
katilingban:General Purpose Functions for Katilingban
To support general and non-specific organisational tasks requiring or supported by R, this package provides general purpose functions that facilitate performant and efficient implementation of standardised workflows. This is particularly useful for website update, newsletter generation, reports, notes and other related tasks that are or will be automated or supported within R.
Maintained by Ernest Guevarra. Last updated 1 years ago.
1 stars 1.70 score
lcbc-uio
eprimeParser:LCBC E-prime data processing pipeline
This package contains functions to process the eprime data for LCBC. The functions are adaptations of scripts James Michael Roe made, that Athanasia Monika Mowinckel converted.
Maintained by Athanasia Mo Mowinckel. Last updated 5 years ago.
1.70 score 1 scriptscran
dbglm:Generalised Linear Models by Subsampling and One-Step Polishing
Fast fitting of generalised linear models on moderately large datasets, by taking an initial sample, fitting in memory, then evaluating the score function for the full data in the database. Thomas Lumley <doi:10.1080/10618600.2019.1610312>.
Maintained by Shangqing Cao. Last updated 4 years ago.
1.70 scoreemptyfield-ds
rrr.workshop:Install Materials for Reproducible Research in R
Install learning materials for Reproducible Research in R.
Maintained by Malcolm Barrett. Last updated 4 years ago.
1.70 score 1 scripts
rogiersbart
bro:My personal R tools
This package collects some functions I created for myself to facilitate certain tasks. I do not expect it to be very useful for anyone else, but if you think this can help you out, be my guest!
Maintained by Bart Rogiers. Last updated 7 months ago.
1.70 score 7 scripts
workshop-brg
abmR:Agent-Based Models in R
Supplies tools for running agent-based models (ABM) in R, as discussed in Gochanour et al. (2022) <doi:10.1111/2041-210X.14014>. The package contains two movement functions, each of which is based on the Ornstein-Uhlenbeck (OU) model (Ornstein & Uhlenbeck, 1930) <doi:10.1103/PhysRev.36.823>. It also contains several visualization and data summarization functions to facilitate the presentation of simulation results.
Maintained by Benjamin Gochanour. Last updated 2 years ago.
1 stars 1.70 scoreselesnow
galigor:Collection of Packages for Internet Marketing
Collection of packages for work with API 'Google Ads' <https://developers.google.com/google-ads/api/docs/start>, 'Yandex Direct' <https://yandex.ru/dev/direct/>, 'Yandex Metrica' <https://yandex.ru/dev/metrika/>, 'MyTarget' <https://target.my.com/help/advertisers/api_arrangement/ru>, 'Vkontakte' <https://vk.com/dev/methods>, 'Facebook' <https://developers.facebook.com/docs/marketing-apis/> and 'AppsFlyer' <https://support.appsflyer.com/hc/en-us/articles/207034346-Using-Pull-API-aggregate-data>. This packages allows you loading data from ads account and manage your ads materials.
Maintained by Alexey Seleznev. Last updated 4 years ago.
1.70 score 2 scriptspanukatan
openmarawi:An Interface to Open Marawi Database
The citizens of Marawi have a right to the data and maps about their home city. When problems are complex, helping people find useful maps (access) can aid them both in finding themselves in the map (understanding) and making the map by themselves (ownership). Open data and useful maps can help empower citizens in mapmaking, placemaking, and decision-making because it can help citizens and interested parties in understanding the issues spatially. It is practical in deliberating, deciding, and delivering the rehabilitation of Marawi City.
Maintained by Ernest Guevarra. Last updated 1 years ago.
1 stars 1.70 score
marsicofl
forensIT:Information Theory Tools for Forensic Analysis
The 'forensIT' package is a comprehensive statistical toolkit tailored for handling missing person cases. By leveraging information theory metrics, it enables accurate assessment of kinship, particularly when limited genetic evidence is available. With a focus on optimizing statistical power, 'forensIT' empowers investigators to effectively prioritize family members, enhancing the reliability and efficiency of missing person investigations.
Maintained by Franco Marsico. Last updated 2 months ago.
1.70 score 1 scriptspredictiveecology
usefulFuns:Useful functions for my modules and packages
A few functions and wrappers around useful code.
Maintained by Tati Micheletti. Last updated 4 months ago.
1.70 score 1 scriptscran
crops:Changepoints for a Range of Penalties (CROPS)
Implements the Changepoints for a Range of Penalties (CROPS) algorithm of Haynes et al. (2017) <doi:10.1080/10618600.2015.1116445> for finding all of the optimal segmentations for multiple penalty values over a continuous range.
Maintained by Daniel Grose. Last updated 3 years ago.
1.48 score 1 dependents
diprosinha
EpiSemble:Ensemble Based Machine Learning Approach for Predicting Methylation States
DNA methylation (6mA) is a major epigenetic process by which alteration in gene expression took place without changing the DNA sequence. Predicting these sites in-vitro is laborious, time consuming as well as costly. This 'EpiSemble' package is an in-silico pipeline for predicting DNA sequences containing the 6mA sites. It uses an ensemble-based machine learning approach by combining Support Vector Machine (SVM), Random Forest (RF) and Gradient Boosting approach to predict the sequences with 6mA sites in it. This package has been developed by using the concept of Chen et al. (2019) <doi:10.1093/bioinformatics/btz015>.
Maintained by Dipro Sinha. Last updated 2 years ago.
1 stars 1.00 score 5 scriptscran
polimetrics:R Tools for Political Measures
This is a collection of data and functions for common metrics in political science research. Data measuring ideology, and functions calculating geographical diffusion and ideological diffusion - geog.diffuse() and ideo.dist(), respectively. Functions derived from methods developed in: Soule and King (2006) <doi:10.1086/499908>, Berry et al. (1998) <doi:10.2307/2991759>, Cruz-Aceves and Mallinson (2019) <doi:10.1177/0160323X20902818>, and Grossback et al. (2004) <doi:10.1177/1532673X04263801>.
Maintained by Vann Jr Burrel. Last updated 3 years ago.
1.00 scorecran
WinRatio:Win Ratio for Prioritized Outcomes and 95% Confidence Interval
Calculate the win ratio for prioritized outcomes and the 95% confidence interval based on Bebu and Lachin (2016) <doi:10.1093/biostatistics/kxv032>. Three type of outcomes can be analyzed: survival "failure-time" events, repeated survival "failure-time" events and continuous or ordinal "non-failure time" events that are captured at specific time-points in the study.
Maintained by Kevin Duarte. Last updated 4 years ago.
1.00 score
nicolasv-dev
drimmR:Estimation, Simulation and Reliability of Drifting Markov Models
Performs the drifting Markov models (DMM) which are non-homogeneous Markov models designed for modeling the heterogeneities of sequences in a more flexible way than homogeneous Markov chains or even hidden Markov models. In this context, we developed an R package dedicated to the estimation, simulation and the exact computation of associated reliability of drifting Markov models. The implemented methods are described in Vergne, N. (2008), <doi:10.2202/1544-6115.1326> and Barbu, V.S., Vergne, N. (2019) <doi:10.1007/s11009-018-9682-8> .
Maintained by Nicolas Vergne. Last updated 4 years ago.
1.00 score
jcochero
optimos.prime:Optimos Prime Helps Calculate Autoecological Data for Biological Species
Calculates autoecological data (optima and tolerance ranges) of a biological species given an environmental matrix. The package calculates by weighted averaging, using the number of occurrences to adjust the tolerance assigned to each taxon to estimate optima and tolerance range in cases where taxa have unequal occurrences. See the detailed methodology by Birks et al. (1990) <doi:10.1098/rstb.1990.0062>, and a case example by Potapova and Charles (2003) <doi:10.1046/j.1365-2427.2003.01080.x>.
Maintained by Joaquín Cochero. Last updated 5 years ago.
1.00 score 2 scriptsdiprosinha
GB5mcPred:Gradient Boosting Algorithm for Predicting Methylation States
DNA methylation of 5-methylcytosine (5mC) is the result of a multi-step, enzyme-dependent process. Predicting these sites in-vitro is laborious, time consuming as well as costly. This ' Gb5mC-Pred ' package is an in-silico pipeline for predicting DNA sequences containing the 5mC sites. It uses a machine learning approach which uses Stochastic Gradient Boosting approach for prediction of the sequences with 5mC sites. This package has been developed by using the concept of Navarez and Roxas (2022) <doi:10.1109/TCBB.2021.3082184>.
Maintained by Dipro Sinha. Last updated 2 years ago.
1.00 score 3 scripts
imiqbal
ImFoR:Non-Linear Height Diameter Models for Forestry
Tree height is an important dendrometric variable and forms the basis of vertical structure of a forest stand. This package will help to fit and validate various non-linear height diameter models for assessing the underlying relationship that exists between tree height and diameter at breast height in case of conifer trees. This package has been implemented on Naslund, Curtis, Michailoff, Meyer, Power, Michaelis-Menten and Wykoff non linear models using algorithm of Huang et al. (1992) <doi:10.1139/x92-172> and Zeide et al. (1993) <doi:10.1093/forestscience/39.3.594>.
Maintained by M. Iqbal Jeelani. Last updated 2 years ago.
1.00 scorecran
soilassessment:Soil Health Assessment Models for Assessing Soil Conditions and Suitability
Soil health assessment builds information to improve decision in soil management. It facilitates assessment of soil conditions for crop suitability [such as those given by FAO <https://www.fao.org/land-water/databases-and-software/crop-information/en/>], groundwater recharge, fertility, erosion, salinization [<doi:10.1002/ldr.4211>], carbon sequestration, irrigation potential, and status of soil resources.
Maintained by Christian Thine Omuto. Last updated 3 months ago.
1 stars 1.00 scorecran
icertool:Calculate and Plot ICER
The app will calculate the ICER (incremental cost-effectiveness ratio) Rawlins (2012) <doi:10.1016/B978-0-7020-4084-9.00044-6> from the mean costs and quality-adjusted life years (QALY) Torrance and Feeny (2009) <doi:10.1017/S0266462300008461> for a set of treatment options, and draw the efficiency frontier in the costs-effectiveness plane. The app automatically identifies and excludes dominated and extended-dominated options from the ICER calculation.
Maintained by Daniel Perez-Troncoso. Last updated 3 years ago.
1.00 scorecran
Tushare:Interface to 'Tushare Pro' API
Helps the R users to get data from 'Tushare Pro'<https://tushare.pro>. 'Tushare Pro' is a platform as well as a community with a lot of staffs working in financial area. We support financial data such as stock price, financial report statements and digital coins data.
Maintained by Feifei ZHANG. Last updated 3 years ago.
1.00 scorecran
EntropicStatistics:Functions Based on Entropic Statistics
Contains methods for data analysis in entropic perspective. These entropic perspective methods are nonparametric, and perform better on non-ordinal data. Currently, the package has a function HeatMap() for visualizing distributional characteristics among multiple populations (groups).
Maintained by Jialin Zhang (JZ). Last updated 2 years ago.
1.00 score
flankado
Ricrt:Randomization Inference of Clustered Randomized Trials
Methods for randomization inference in group-randomized trials. Specifically, it can be used to analyze the treatment effect of stratified data with multiple clusters in each stratum with treatment given on cluster level. User may also input as many covariates as they want to fit the data. Methods are described by Dylan S Small et al., (2012) <doi:10.1198/016214507000000897>.
Maintained by Yang Dong. Last updated 2 years ago.
1.00 score
atanubhattacharjee
SurvHiDim:High Dimensional Survival Data Analysis
High dimensional time to events data analysis with variable selection technique. Currently support LASSO, clustering and Bonferroni's correction.
Maintained by Atanu Bhattacharjee. Last updated 4 years ago.
1.00 score 1 scriptscran
cpop:Detection of Multiple Changes in Slope in Univariate Time-Series
Detects multiple changes in slope using the CPOP dynamic programming approach of Fearnhead, Maidstone, and Letchford (2019) <doi:10.1080/10618600.2018.1512868>. This method finds the best continuous piecewise linear fit to data under a criterion that measures fit to data using the residual sum of squares, but penalizes complexity based on an L0 penalty on changes in slope. Further information regarding the use of this package with detailed examples can be found in Fearnhead and Grose (2024) <doi:10.18637/jss.v109.i07>.
Maintained by Daniel Grose. Last updated 10 months ago.
1.00 score