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projectmosaic

mosaic:Project MOSAIC Statistics and Mathematics Teaching Utilities

Data sets and utilities from Project MOSAIC (<http://www.mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.

Maintained by Randall Pruim. Last updated 1 years ago.

93 stars 13.32 score 7.2k scripts 7 dependents

bioc

bumphunter:Bump Hunter

Tools for finding bumps in genomic data

Maintained by Tamilselvi Guharaj. Last updated 5 months ago.

dnamethylationepigeneticsinfrastructuremultiplecomparisonimmunooncology

16 stars 11.61 score 210 scripts 43 dependents

r-forge

tuneR:Analysis of Music and Speech

Analyze music and speech, extract features like MFCCs, handle wave files and their representation in various ways, read mp3, read midi, perform steps of a transcription, ... Also contains functions ported from the 'rastamat' 'Matlab' package.

Maintained by Uwe Ligges. Last updated 12 months ago.

7.93 score 1.1k scripts 44 dependents

fawda123

SWMPr:Retrieving, Organizing, and Analyzing Estuary Monitoring Data

Tools for retrieving, organizing, and analyzing environmental data from the System Wide Monitoring Program of the National Estuarine Research Reserve System <https://cdmo.baruch.sc.edu/>. These tools address common challenges associated with continuous time series data for environmental decision making.

Maintained by Marcus W. Beck. Last updated 2 months ago.

13 stars 7.05 score 143 scripts 1 dependents

pcruniversum

chipPCR:Toolkit of Helper Functions to Pre-Process Amplification Data

A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. Contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experimental nucleic acid amplification systems ('VideoScan HCU', capillary convective PCR (ccPCR)) and commercial systems are included. Amplification curves were generated by helicase dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used. For more information see: Roediger et al. (2015) <doi:10.1093/bioinformatics/btv205>.

Maintained by Stefan Roediger. Last updated 4 years ago.

8 stars 6.84 score 97 scripts 1 dependents

helske

bssm:Bayesian Inference of Non-Linear and Non-Gaussian State Space Models

Efficient methods for Bayesian inference of state space models via Markov chain Monte Carlo (MCMC) based on parallel importance sampling type weighted estimators (Vihola, Helske, and Franks, 2020, <doi:10.1111/sjos.12492>), particle MCMC, and its delayed acceptance version. Gaussian, Poisson, binomial, negative binomial, and Gamma observation densities and basic stochastic volatility models with linear-Gaussian state dynamics, as well as general non-linear Gaussian models and discretised diffusion models are supported. See Helske and Vihola (2021, <doi:10.32614/RJ-2021-103>) for details.

Maintained by Jouni Helske. Last updated 7 months ago.

bayesian-inferencecppmarkov-chain-monte-carloparticle-filterstate-spacetime-seriesopenblascppopenmp

42 stars 6.43 score 11 scripts

trackerproject

trackeR:Infrastructure for Running, Cycling and Swimming Data from GPS-Enabled Tracking Devices

Provides infrastructure for handling running, cycling and swimming data from GPS-enabled tracking devices within R. The package provides methods to extract, clean and organise workout and competition data into session-based and unit-aware data objects of class 'trackeRdata' (S3 class). The information can then be visualised, summarised, and analysed through flexible and extensible methods. Frick and Kosmidis (2017) <doi: 10.18637/jss.v082.i07>, which is updated and maintained as one of the vignettes, provides detailed descriptions of the package and its methods, and real-data demonstrations of the package functionality.

Maintained by Ioannis Kosmidis. Last updated 1 years ago.

90 stars 6.37 score 58 scripts 1 dependents

tombeesley

eyetools:Analyse Eye Data

Enables the automation of actions across the pipeline, including initial steps of transforming binocular data and gap repair to event-based processing such as fixations, saccades, and entry/duration in Areas of Interest (AOIs). It also offers visualisation of eye movement and AOI entries. These tools take relatively raw (trial, time, x, and y form) data and can be used to return fixations, saccades, and AOI entries and time spent in AOIs. As the tools rely on this basic data format, the functions can work with data from any eye tracking device. Implements fixation and saccade detection using methods proposed by Salvucci and Goldberg (2000) <doi:10.1145/355017.355028>.

Maintained by Tom Beesley. Last updated 22 hours ago.

areas-of-interestattention-visualizationcognitive-sciencedwell-time-algorithmeye-trackereye-trackingeyetrackingggplot2psychologypsychology-experimentssaccadestobiitobii-eye-trackervisualization

4 stars 5.51 score 8 scripts

fawda123

WtRegDO:Implement Weighted Regression on Dissolved Oxygen Time Series

A sample dataset and functions to implement weighted regression on dissolved oxygen time series are included as a simple example to reduce the effects of tidal advection. Functions are also available to estimate net ecosystem metabolism using the open-water method.

Maintained by Marcus W. Beck. Last updated 10 months ago.

detidingmetabolismweighted-regression

5 stars 3.50 score 42 scripts

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