Showing 8 of total 8 results (show query)
rethomics
behavr:Canonical Data Structure for Behavioural Data
Implements an S3 class based on 'data.table' to store and process efficiently ethomics (high-throughput behavioural) data.
Maintained by Quentin Geissmann. Last updated 4 years ago.
biological-data-analysisdata-structuresethomics
6 stars 5.91 score 64 scripts 7 dependentsrethomics
ggetho:Visualisation of High-Throughput Behavioural (i.e. Ethomics) Data
Extension of 'ggplot2' providing layers, scales and preprocessing functions useful to represent behavioural variables that are recorded over multiple animals and days. This package is part of the 'rethomics' framework <https://rethomics.github.io/>.
Maintained by Quentin Geissmann. Last updated 2 years ago.
biological-data-analysisggplot2visualization
9 stars 4.98 score 71 scripts 1 dependentsrethomics
damr:Interface to Drosophila Activity Monitor System Result Files
Loads behavioural data from the widely used Drosophila Activity Monitor System (DAMS, TriKinetics <https://trikinetics.com/>) into the rethomics framework.
Maintained by Quentin Geissmann. Last updated 12 months ago.
biological-data-analysisparsing
6 stars 4.92 score 31 scripts 1 dependents
bioc
ddPCRclust:Clustering algorithm for ddPCR data
The ddPCRclust algorithm can automatically quantify the CPDs of non-orthogonal ddPCR reactions with up to four targets. In order to determine the correct droplet count for each target, it is crucial to both identify all clusters and label them correctly based on their position. For more information on what data can be analyzed and how a template needs to be formatted, please check the vignette.
Maintained by Benedikt G. Brink. Last updated 5 months ago.
ddpcrclusteringbiological-data-analysis
4 stars 4.60 score 4 scripts
jonathanrd
pbm:Protein Binding Models
Binding models which are useful when analysing protein-ligand interactions by techniques such as Biolayer Interferometry (BLI) or Surface Plasmon Resonance (SPR). Naman B. Shah, Thomas M. Duncan (2014) <doi:10.3791/51383>. Hoang H. Nguyen et al. (2015) <doi:10.3390/s150510481>. After initial binding parameters are known, binding curves can be simulated and parameters can be varied. The models within this package may also be used to fit a curve to measured binding data using non-linear regression.
Maintained by Jonathan Davies. Last updated 4 years ago.
biological-data-analysisbiologyprotein-protein-interaction
3 stars 4.41 score 17 scriptsrethomics
sleepr:Analyse Activity and Sleep Behaviour
Use behavioural variables to score activity and infer sleep from bouts of immobility. It is primarily designed to score sleep in fruit flies from Drosophila Activity Monitor (TriKinetics) and Ethoscope data. It implements sleep scoring using the "five-minute rule" (Hendricks et al. (2000) <DOI:10.1016/S0896-6273(00)80877-6>), activity classification for Ethoscopes (Geissmann et al. (2017) <DOI:10.1371/journal.pbio.2003026>) and a new algorithm to detect when animals are dead.
Maintained by Quentin Geissmann. Last updated 3 years ago.
biological-data-analysisneuroscience
6 stars 4.27 score 62 scripts
zcolburn
Bioi:Biological Image Analysis
Single linkage clustering and connected component analyses are often performed on biological images. 'Bioi' provides a set of functions for performing these tasks. This functionality is implemented in several key functions that can extend to from 1 to many dimensions. The single linkage clustering method implemented here can be used on n-dimensional data sets, while connected component analyses are limited to 3 or fewer dimensions.
Maintained by Zachary Colburn. Last updated 5 years ago.
biological-data-analysisbiologycellcppimage-analysismicroscopycpp
3.81 score 13 scriptsrethomics
scopr:Read Ethoscope Data
Handling of behavioural data from the Ethoscope platform (Geissmann, Garcia Rodriguez, Beckwith, French, Jamasb and Gilestro (2017) <DOI:10.1371/journal.pbio.2003026>). Ethoscopes (<http://gilestrolab.github.io/ethoscope/>) are an open source/open hardware framework made of interconnected raspberry pis (<https://www.raspberrypi.org>) designed to quantify the behaviour of multiple small animals in a distributed and real-time fashion. The default tracking algorithm records primary variables such as xy coordinates, dimensions and speed. This package is part of the rethomics framework <http://rethomics.github.io/>.
Maintained by Quentin Geissmann. Last updated 3 years ago.
biological-data-analysisparsing
3 stars 3.18 score