John Muschelli

John Muschelli

39 packages on CRAN

2 packages on GitHub

rscopus

cran
93th

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

brainR

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89th

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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>).

matlabr

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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.

diffr

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87th

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An R interface to the 'codediff' JavaScript library (a copy of which is included in the package). Allows for visualization of the difference between 2 files, usually text files or R scripts, in a browser.

gcite

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87th

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

mscstts

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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://www.microsoft.com/cognitive-services/> in order to obtain a (free) API key. Without an API key, this package will not work properly.

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

neurobase

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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.

spm12r

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Installs 'SPM12' to the R library directory and has associated functions for 'fMRI' and general imaging utilities, called through 'MATLAB'.

fslr

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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.

neurohcp

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

glassdoor

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81th

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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.

77th

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Unifies different text to speech engines, such as Google, Microsoft, and Amazon. Text synthesis can be done in any engine with a simple switch of an argument denoting the service requested.

freesurfer

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61th

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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.

kirby21.t1

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

cifti

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

53th

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Downloads data from Federal 'RePORTER' <https://api.federalreporter.nih.gov/> using the Federal 'RePORTER' API. Allows the user to search job projects from different government agencies.

gifti

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

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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.

papayar

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43th

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Users pass images and objects of class 'nifti' from the 'oro.nifti' package to a Papaya, an interactive lightweight JavaScript viewer. Although many packages can view individual slices or projections of image and matrix data, this package allows for quick and easy interactive browsing of images. The viewer is based off of the Mango software, which is a lightweight medical image viewer.

stapler

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34th

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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.

leanpubr

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28th

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Provides access to the 'Leanpub' API <https://leanpub.com/help/api> for gathering information about publications and submissions to the 'Leanpub' platform.

nsrr

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Allows users to access data from the National Sleep Research Resource ('NSRR') <https://sleepdata.org/>.

neurovault

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Uses 'Neurovault' API <https://neurovault.org/api-docs> to download statistical maps of the human brain stored on that platform.

knitr

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Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

rticles

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A suite of custom R Markdown formats and templates for authoring journal articles and conference submissions.

oro.nifti

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Functions for the input/output and visualization of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats. This package is part of the Rigorous Analytics bundle.

tuber

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89th

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Get comments posted on YouTube videos, information on how many times a video has been liked, search for videos with particular content, and much more. You can also scrape captions from a few videos. To learn more about the YouTube API, see <https://developers.google.com/youtube/v3/>.

runstats

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81th

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Provides methods for fast computation of running sample statistics for time series. These include: (1) mean, (2) standard deviation, and (3) variance over a fixed-length window of time-series, (4) correlation, (5) covariance, and (6) Euclidean distance (L2 norm) between short-time pattern and time-series. Implemented methods utilize Convolution Theorem to compute convolutions via Fast Fourier Transform (FFT).

sublime

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79th

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Creates probability maps of incident and enlarging lesion voxels from a baseline and followup magnetic resonance imaging study in patients with multiple sclerosis.

77th

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Read raw accelerometry from 'GT3X+' data and plain table data to calculate Activity Index from Bai et al. (2016) <doi:10.1371/journal.pone.0160644>.

nitrcbot

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Parses and downloads images from various 'NeuroImaging Tools and Resources Collaboratory' <https://www.nitrc.org> sets.

ari

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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.

crsra

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53th

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Tidies and performs preliminary analysis of 'Coursera' research export data. These export data can be downloaded by anyone who has classes on Coursera and wants to analyze the data. Coursera is one of the leading providers of MOOCs and was launched in January 2012. With over 25 million learners, Coursera is the most popular provider in the world being followed by EdX, the MOOC provider that was a result of a collaboration between Harvard University and MIT, with over 10 million users. Coursera has over 150 university partners from 29 countries and offers a total of 2000+ courses from computer science to philosophy. Besides, Coursera offers 180+ specialization, Coursera's credential system, and four fully online Masters degrees. For more information about Coursera check Coursera's About page on <https://blog.coursera.org/about/>.

scifigure

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43th

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Users may specify what fundamental qualities of a new study have or have not changed in an attempt to reproduce or replicate an original study. A comparison of the differences is visualized. Visualization approach follows 'Patil', 'Peng', and 'Leek' (2016) <doi:10.1101/066803>.

oasis

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34th

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Trains and makes predictions from the OASIS method, described in detail in the paper "OASIS is Automated Statistical Inference for Segmentation, with applications to multiple sclerosis lesion segmentation in MRI" <doi:10.1016/j.nicl.2013.03.002>. OASIS is a method for multiple sclerosis (MS) lesion segmentation on structural magnetic resonance image (MRI) studies. OASIS creates probability maps of lesion presence using the FLAIR, T2, T1, and PD structural MRI volumes. This packages allows for training of the OASIS model and prediction of OASIS probability maps from a trained model with user supplied studies that have a gold standard lesion segmentation masks. The package will also create OASIS probability maps for MRI studies using the OASIS model from the OASIS paper if no gold standard lesion segmentation masks are available.

spant

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Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data.

adept

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14th

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Designed for optimal use in performing fast, accurate walking strides segmentation from high-density data collected from a wearable accelerometer worn during continuous walking activity.

gganatogram

github
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Create anatograms, tool that enables the user to visualize data sets directly on representations of a body of various species. These are commonly used to graphically explore large-scale human gene expression data.

Rvision

github
14th

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This package uses the OpenCV library to provide R users with methods to read and manipulate video and image files, as well as camera streams.