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rscopus - Scopus Database 'API' Interface

Uses Elsevier 'Scopus' API <https://dev.elsevier.com/sc_apis.html> to download information about authors and their citations.

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bibliometricsscopusscopus-api

9.67 score 85 stars 3 dependents 174 scripts 12k downloads

neurobase - 'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects

Base package for 'Neuroconductor', which includes many helper functions that interact with objects of class 'nifti', implemented by package 'oro.nifti', for reading/writing and also other manipulation functions.

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8.28 score 7 stars 5 dependents 598 scripts 863 downloads

freesurfer - Wrapper Functions for 'FreeSurfer'

Wrapper functions that interface with 'Freesurfer' <https://surfer.nmr.mgh.harvard.edu/>, a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'Freesurfer' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'Freesurfer' command and returns an R object of class 'nifti' or necessary output.

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8.25 score 10 stars 88 scripts 471 downloads

fslr - Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

Wrapper functions that interface with 'FSL' <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>, a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'FSL' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'FSL' command and returns an R object of class 'nifti' if desired.

Last updated

fslfslrneuroimagingneuroimaging-analysisneuroimaging-data-science

7.88 score 46 stars 556 scripts 604 downloads

gifti - Reads in 'Neuroimaging' 'GIFTI' Files with Geometry Information

Functions to read in the geometry format under the 'Neuroimaging' 'Informatics' Technology Initiative ('NIfTI'), called 'GIFTI' <https://www.nitrc.org/projects/gifti/>. These files contain surfaces of brain imaging data.

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7.75 score 4 stars 12 dependents 115 scripts 1.7k downloads

diffr - Display Differences Between Two Files using Codediff Library

An R interface to the 'codediff' JavaScript library (a copy of which is included in the package, see <https://github.com/danvk/codediff.js> for information). Allows for visualization of the difference between 2 files, usually text files or R scripts, in a browser.

Last updated

6.37 score 67 stars 3 dependents 77 scripts 619 downloads

WhiteStripe - White Matter Normalization for Magnetic Resonance Images

Shinohara (2014) <doi:10.1016/j.nicl.2014.08.008> introduced 'WhiteStripe', an intensity-based normalization of T1 and T2 images, where normal appearing white matter performs well, but requires segmentation. This method performs white matter mean and standard deviation estimates on data that has been rigidly-registered to the 'MNI' template and uses histogram-based methods.

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6.31 score 9 stars 75 scripts 403 downloads

actiread - Baseline Package for Reading Actigraphy and Activity Data

Provides baseline functions for reading actigraphy and activity data, relying on baseline functions from 'actibase'. Reads data from 'Axivity' 'CWA' <https://axivity.com/> , ActiGraph 'GT3X' <https://ametris.com/actigraph-wgt3x-bt>, 'SensorLog' <https://sensorlog.berndthomas.net/>, and 'SensorLogger' <https://www.tszheichoi.com/sensorlogger> zipped CSV files.

Last updated

5.72 score 2 dependents 16 scripts 410 downloads

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', the 'Speechify Text-to-Speech API', and a free TTS engine called 'Coqui TTS'.

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edtech-softwarespeech-synthesistext-to-speechttsvoice

5.72 score 21 stars 77 downloads

matlabr - An Interface for MATLAB using System Calls

Provides users to call MATLAB from using the "system" command. Allows users to submit lines of code or MATLAB m files. This is in comparison to 'R.matlab', which creates a MATLAB server.

Last updated

5.68 score 13 stars 2 dependents 124 scripts 462 downloads

neurohcp - Human 'Connectome' Project Interface

Downloads and reads data from Human 'Connectome' Project <https://balsa.wustl.edu/> using Amazon Web Services ('AWS') 'S3' buckets.

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5.39 score 9 stars 55 scripts 415 downloads

mapnhanespa - Map Quantiles for Physical Activity from 'NHANES'

Maps physical activity from the National Health and Nutrition Examination Survey ('NHANES') study into population-based quantiles.

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5.13 score 1 dependents 5 scripts 252 downloads

actibase - Baseline Functions for Actigraphy and Activity Processing and Analysis

Provides baseline functions for actigraphy and activity data. This package is intended to be extended by downstream overlays such as 'actiread', 'actimetrics', and 'stepcount'.

Last updated

4.86 score 4 dependents 11 scripts 603 downloads

actimetrics - Create Metrics Actigraphy and Activity Analysis

Provides functions for calibrating, counting, and summarizing actigraphy and activity data into specific metrics and sleep measures. The metrics include activity counts, step counts, activity index, Monitor Independent Movement Summary Unit (MIMS), mean amplitude deviation (MAD), and provides wrappers for sleep estimation from activity counts using Tudor-Locke (2014) <doi:10.1139/apnm-2013-0173> and Sadeh (1994) <doi:10.1093/sleep/17.3.201>.

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4.78 score 6 scripts 559 downloads

glassdoor - Interface to 'Glassdoor' API

Interacts with the 'Glassdoor' API <https://www.glassdoor.com/developer/index.htm>. Allows the user to search job statistics, employer statistics, and job progression, where 'Glassdoor' provides a breakdown of other jobs a person did after their current one.

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4.75 score 7 stars 16 scripts 402 downloads

brainR - Helper Functions to 'misc3d' and 'rgl' Packages for Brain Imaging

This includes functions for creating 3D and 4D images using 'WebGL', 'rgl', and 'JavaScript' commands. This package relies on the X toolkit ('XTK', <https://github.com/xtk/X#readme>).

Last updated

4.64 score 12 stars 1 dependents 24 scripts 377 downloads

cifti - Toolbox for Connectivity Informatics Technology Initiative ('CIFTI') Files

Functions for the input/output and visualization of medical imaging data in the form of 'CIFTI' files <https://www.nitrc.org/projects/cifti/>.

Last updated

4.53 score 3 stars 114 scripts 489 downloads

actiwalkability - Access the EPA Walkability Index

Provides helpers for querying the EPA Walkability Index <https://www.epa.gov/smartgrowth/national-walkability-index-user-guide-and-methodology> and working with Census GEOID/FIPS identifiers <https://www.census.gov/programs-surveys/geography/guidance/geo-identifiers.html>.

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4.30 score 1 stars 4 scripts 495 downloads

walking - Segments Accelerometry Data into Walking Bouts using Open Source Methods

Segments walking from accelerometry data using 'forest' python module <https://github.com/onnela-lab/forest> from Yi (2025) <doi:10.2196/71375>, 'Verisense' original from Rowlands (2022) <doi:10.1080/02640414.2022.2147134> and 'Verisense' revised from Maylor (2022) <doi:10.3390/s22249984>, and Step Detection Threshold (SDT) from Ducharme (2021) <doi:10.1123/jmpb.2021-0011> methods.

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4.26 score 1 stars 1 dependents 15 scripts 272 downloads

gcite - Google Citation Parser

Scrapes Google Citation pages and creates data frames of citations over time.

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3.76 score 3 stars 38 scripts 258 downloads

stapler - Simultaneous Truth and Performance Level Estimation

An implementation of Simultaneous Truth and Performance Level Estimation (STAPLE) <doi:10.1109/TMI.2004.828354>. This method is used when there are multiple raters for an object, typically an image, and this method fuses these ratings into one rating. It uses an expectation-maximization method to estimate this rating and the individual specificity/sensitivity for each rater.

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3.74 score 1 stars 11 scripts 281 downloads

mscstts - R Client for the Microsoft Cognitive Services 'Text-to-Speech' REST API

R Client for the Microsoft Cognitive Services 'Text-to-Speech' REST API, including voice synthesis. A valid account must be registered at the Microsoft Cognitive Services website <https://azure.microsoft.com/en-us/products/ai-services/> in order to obtain a (free) API key. Without an API key, this package will not work properly.

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3.72 score 8 stars 13 scripts 340 downloads

asleep - Estimate Sleep from 'Accelerometry' Data

Interfaces the 'asleep' python module <https://github.com/OxWearables/asleep> from Yuan (2024) <doi:10.1038/s41746-024-01148-y> to estimate sleep from 'accelerometry' data.

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3.60 score 5 scripts 365 downloads

kirby21.base - Example Data from the Multi-Modal MRI 'Reproducibility' Resource

Multi-modal magnetic resonance imaging ('MRI') data from the 'Kirby21' 'reproducibility' study <https://www.nitrc.org/projects/multimodal/>, including functional and structural imaging.

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3.58 score 2 dependents 63 scripts 253 downloads

actisensorlog - Summarize 'SensorLog'/'SensorLogger' Activity Data

Provides functions for analyzing 'SensorLog' <https://sensorlog.berndthomas.net/> and 'SensorLogger' <https://www.tszheichoi.com/sensorlogger> data.

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3.48 score 1 stars 3 scripts 408 downloads

kirby21.t1 - Example T1 Structural Data from the Multi-Modal MRI 'Reproducibility' Resource

Structural T1 magnetic resonance imaging ('MRI') data from the 'Kirby21' 'reproducibility' study <doi:10.1016/j.neuroimage.2010.11.047>.

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3.43 score 54 scripts 315 downloads

actinet - Estimate Human Activity from Accelerometry Data

Interfaces the 'actinet' Python module <https://github.com/OxWearables/actinet> for an activity classification model based on self-supervised learning for wrist-worn accelerometer data.

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3.40 score 4 scripts 414 downloads

kirby21.fmri - Example Functional Imaging Data from the Multi-Modal MRI 'Reproducibility' Resource

Functional magnetic resonance imaging ('fMRI') data from the 'Kirby21' 'reproducibility' study <doi:10.1016/j.neuroimage.2010.11.047>.

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3.31 score 41 scripts 202 downloads

actiquantiles - Map Activity Data to Normalized Quantiles

Provides functions mapping physical activity measures to normalized quantiles. Currently, only maps the 'NHANES' quantiles, but other quantiles will be integrated.

Last updated

3.18 score 2 scripts 346 downloads

cforward - Forward Selection using Concordance/C-Index

Performs forward model selection, using the C-index/concordance in survival analysis models.

Last updated

2.70 score 3 scripts 238 downloads