R-universe search: imaging

asgr

imager:Image Processing Library Based on 'CImg'

Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.

Maintained by Aaron Robotham. Last updated 27 days ago.

libx11 fftw3 tiff cpp openmp

261.8 match 17 stars 13.62 score 2.4k scripts 45 dependents

spatstat

spatstat.geom:Geometrical Functionality of the 'spatstat' Family

Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)

Maintained by Adrian Baddeley. Last updated 2 days ago.

classes-and-objects distance-calculation geometry geometry-processing images mensuration plotting point-patterns spatial-data spatial-data-analysis

128.9 match 7 stars 12.11 score 241 scripts 227 dependents

muschellij2

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.

Maintained by John Muschelli. Last updated 1 months ago.

fsl fslr neuroimaging neuroimaging-analysis neuroimaging-data-science

154.0 match 41 stars 8.01 score 420 scripts

bjw34032

oro.nifti:Rigorous - 'NIfTI' + 'ANALYZE' + 'AFNI' : Input / Output

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.

Maintained by Brandon Whitcher. Last updated 6 months ago.

afni analyze nifti

146.1 match 2 stars 7.70 score 764 scripts 38 dependents

ropensci

magick:Advanced Graphics and Image-Processing in R

Bindings to 'ImageMagick': the most comprehensive open-source image processing library available. Supports many common formats (png, jpeg, tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio images are automatically previewed when printed to the console, resulting in an interactive editing environment. The latest version of the package includes a native graphics device for creating in-memory graphics or drawing onto images using pixel coordinates.

Maintained by Jeroen Ooms. Last updated 20 days ago.

image-manipulation image-processing imagemagick cpp

61.6 match 468 stars 17.31 score 9.0k scripts 256 dependents

muschellij2

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.

Maintained by John Muschelli. Last updated 1 months ago.

104.4 match 5 stars 8.49 score 486 scripts 7 dependents

bioc

EBImage:Image processing and analysis toolbox for R

EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.

Maintained by Andrzej Oleś. Last updated 5 months ago.

visualization bioinformatics image-analysis image-processing cpp

64.8 match 71 stars 12.89 score 1.5k scripts 33 dependents

rstudio

keras3:R Interface to 'Keras'

Interface to 'Keras' <https://keras.io>, a high-level neural networks API. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both CPU and GPU devices.

Maintained by Tomasz Kalinowski. Last updated 4 days ago.

60.5 match 845 stars 13.57 score 264 scripts 2 dependents

mlampros

OpenImageR:An Image Processing Toolkit

Incorporates functions for image preprocessing, filtering and image recognition. The package takes advantage of 'RcppArmadillo' to speed up computationally intensive functions. The histogram of oriented gradients descriptor is a modification of the 'findHOGFeatures' function of the 'SimpleCV' computer vision platform, the average_hash(), dhash() and phash() functions are based on the 'ImageHash' python library. The Gabor Feature Extraction functions are based on 'Matlab' code of the paper, "CloudID: Trustworthy cloud-based and cross-enterprise biometric identification" by M. Haghighat, S. Zonouz, M. Abdel-Mottaleb, Expert Systems with Applications, vol. 42, no. 21, pp. 7905-7916, 2015, <doi:10.1016/j.eswa.2015.06.025>. The 'SLIC' and 'SLICO' superpixel algorithms were explained in detail in (i) "SLIC Superpixels Compared to State-of-the-art Superpixel Methods", Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Suesstrunk, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 34, num. 11, p. 2274-2282, May 2012, <doi:10.1109/TPAMI.2012.120> and (ii) "SLIC Superpixels", Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Suesstrunk, EPFL Technical Report no. 149300, June 2010.

Maintained by Lampros Mouselimis. Last updated 2 years ago.

filtering gabor-feature-extraction gabor-filters hog-features image image-hashing processing rcpparmadillo recognition slic slico superpixels openblas cpp openmp

76.3 match 60 stars 9.86 score 358 scripts 8 dependents

mlverse

torchvision:Models, Datasets and Transformations for Images

Provides access to datasets, models and preprocessing facilities for deep learning with images. Integrates seamlessly with the 'torch' package and it's 'API' borrows heavily from 'PyTorch' vision package.

Maintained by Daniel Falbel. Last updated 6 months ago.

75.5 match 65 stars 9.74 score 313 scripts 6 dependents

dnychka

fields:Tools for Spatial Data

For curve, surface and function fitting with an emphasis on splines, spatial data, geostatistics, and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance function parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range parameter). A major feature is that any covariance function implemented in R and following a simple format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details as a companion to the manual pages. The commented source code can be viewed by expanding the source code version and looking in the R subdirectory. The reference for fields can be generated by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development of this package was supported in part by the National Science Foundation Grant 1417857, the National Center for Atmospheric Research, and Colorado School of Mines. See the Fields URL for a vignette on using this package and some background on spatial statistics.

Maintained by Douglas Nychka. Last updated 9 months ago.

fortran

57.4 match 15 stars 12.60 score 7.7k scripts 295 dependents

nepem-ufsc

pliman:Tools for Plant Image Analysis

Tools for both single and batch image manipulation and analysis (Olivoto, 2022 <doi:10.1111/2041-210X.13803>) and phytopathometry (Olivoto et al., 2022 <doi:10.1007/S40858-021-00487-5>). The tools can be used for the quantification of leaf area, object counting, extraction of image indexes, shape measurement, object landmark identification, and Elliptical Fourier Analysis of object outlines (Claude (2008) <doi:10.1007/978-0-387-77789-4>). The package also provides a comprehensive pipeline for generating shapefiles with complex layouts and supports high-throughput phenotyping of RGB, multispectral, and hyperspectral orthomosaics. This functionality facilitates field phenotyping using UAV- or satellite-based imagery.

Maintained by Tiago Olivoto. Last updated 2 days ago.

openblas fftw3 cpp openmp

94.3 match 10 stars 6.68 score 476 scripts

bioc

Cardinal:A mass spectrometry imaging toolbox for statistical analysis

Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.

Maintained by Kylie Ariel Bemis. Last updated 3 months ago.

software infrastructure proteomics lipidomics massspectrometry imagingmassspectrometry immunooncology normalization clustering classification regression

53.2 match 47 stars 10.34 score 200 scripts

t-kalinowski

keras:R Interface to 'Keras'

Interface to 'Keras' <https://keras.io>, a high-level neural networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.

Maintained by Tomasz Kalinowski. Last updated 11 months ago.

42.0 match 10.82 score 10k scripts 54 dependents

bioc

cytomapper:Visualization of highly multiplexed imaging data in R

Highly multiplexed imaging acquires the single-cell expression of selected proteins in a spatially-resolved fashion. These measurements can be visualised across multiple length-scales. First, pixel-level intensities represent the spatial distributions of feature expression with highest resolution. Second, after segmentation, expression values or cell-level metadata (e.g. cell-type information) can be visualised on segmented cell areas. This package contains functions for the visualisation of multiplexed read-outs and cell-level information obtained by multiplexed imaging technologies. The main functions of this package allow 1. the visualisation of pixel-level information across multiple channels, 2. the display of cell-level information (expression and/or metadata) on segmentation masks and 3. gating and visualisation of single cells.

Maintained by Lasse Meyer. Last updated 5 months ago.

immunooncology software singlecell onechannel twochannel multiplecomparison normalization dataimport bioimaging imaging-mass-cytometry single-cell spatial-analysis

45.1 match 32 stars 9.61 score 354 scripts 5 dependents

natverse

nat:NeuroAnatomy Toolbox for Analysis of 3D Image Data

NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).

Maintained by Gregory Jefferis. Last updated 5 months ago.

3d connectomics image-analysis neuroanatomy neuroanatomy-toolbox neuron neuron-morphology neuroscience visualisation

40.2 match 67 stars 9.94 score 436 scripts 2 dependents

hiweller

recolorize:Color-Based Image Segmentation

Automatic, semi-automatic, and manual functions for generating color maps from images. The idea is to simplify the colors of an image according to a metric that is useful for the user, using deterministic methods whenever possible. Many images will be clustered well using the out-of-the-box functions, but the package also includes a toolbox of functions for making manual adjustments (layer merging/isolation, blurring, fitting to provided color clusters or those from another image, etc). Also includes export methods for other color/pattern analysis packages (pavo, patternize, colordistance).

Maintained by Hannah Weller. Last updated 13 days ago.

46.5 match 39 stars 7.68 score 87 scripts

ropensci

ijtiff:Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files

General purpose TIFF file I/O for R users. Currently the only such package with read and write support for TIFF files with floating point (real-numbered) pixels, and the only package that can correctly import TIFF files that were saved from 'ImageJ' and write TIFF files than can be correctly read by 'ImageJ' <https://imagej.net/ij/>. Also supports text image I/O.

Maintained by Rory Nolan. Last updated 6 days ago.

image-manipulation imagej peer-reviewed tiff-files tiff-images tiff

39.7 match 18 stars 8.97 score 36 scripts 7 dependents

bbuchsbaum

neuroim:Data Structures and Handling for Neuroimaging Data

A collection of data structures that represent volumetric brain imaging data. The focus is on basic data handling for 3D and 4D neuroimaging data. In addition, there are function to read and write NIFTI files and limited support for reading AFNI files.

Maintained by Bradley Buchsbaum. Last updated 4 years ago.

cpp

62.9 match 6 stars 5.64 score 48 scripts

nplatonov

ursa:Non-Interactive Spatial Tools for Raster Processing and Visualization

S3 classes and methods for manipulation with georeferenced raster data: reading/writing, processing, multi-panel visualization.

Maintained by Nikita Platonov. Last updated 11 months ago.

100.0 match 7 stars 3.54 score 5 scripts

jniedballa

camtrapR:Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses

Management of and data extraction from camera trap data in wildlife studies. The package provides a workflow for storing and sorting camera trap photos (and videos), tabulates records of species and individuals, and creates detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it can visualise species activity data and provides simple mapping functions with GIS export.

Maintained by Juergen Niedballa. Last updated 3 months ago.

occupancy-modeling spatial-capture-recapture wildlife

40.9 match 35 stars 8.65 score 178 scripts

r-spatial

rgee:R Bindings for Calling the 'Earth Engine' API

Earth Engine <https://earthengine.google.com/> client library for R. All of the 'Earth Engine' API classes, modules, and functions are made available. Additional functions implemented include importing (exporting) of Earth Engine spatial objects, extraction of time series, interactive map display, assets management interface, and metadata display. See <https://r-spatial.github.io/rgee/> for further details.

Maintained by Cesar Aybar. Last updated 4 days ago.

earth-engine earthengine google-earth-engine googleearthengine spatial-analysis spatial-data

24.5 match 715 stars 13.77 score 1.9k scripts 3 dependents

bioc

SpatialFeatureExperiment:Integrating SpatialExperiment with Simple Features in sf

A new S4 class integrating Simple Features with the R package sf to bring geospatial data analysis methods based on vector data to spatial transcriptomics. Also implements management of spatial neighborhood graphs and geometric operations. This pakage builds upon SpatialExperiment and SingleCellExperiment, hence methods for these parent classes can still be used.

Maintained by Lambda Moses. Last updated 1 months ago.

datarepresentation transcriptomics spatial

35.4 match 49 stars 9.40 score 322 scripts 1 dependents

bnosac

image.CannyEdges:Implementation of the Canny Edge Detector for Images

An implementation of the Canny Edge Detector for detecting edges in images. The package provides an interface to the algorithm available at <https://github.com/Neseb/canny>.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf fftw3 cpp

61.3 match 278 stars 5.14 score 6 scripts

bnosac

image.LineSegmentDetector:Detect Line Segments in Images

An implementation of the Line Segment Detector on digital images described in the paper: "LSD: A Fast Line Segment Detector with a False Detection Control" by Rafael Grompone von Gioi et al (2012). The algorithm is explained at <doi:10.5201/ipol.2012.gjmr-lsd>.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp

60.8 match 279 stars 5.14 score 7 scripts

bnosac

image.ContourDetector:Implementation of the Unsupervised Smooth Contour Line Detection for Images

An implementation of the Unsupervised Smooth Contour Detection algorithm for digital images as described in the paper: "Unsupervised Smooth Contour Detection" by Rafael Grompone von Gioi, and Gregory Randall (2016). The algorithm is explained at <doi:10.5201/ipol.2016.175>.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp

60.5 match 279 stars 5.14 score 7 scripts

bnosac

image.CornerDetectionF9:Find Corners in Digital Images with FAST-9

An implementation of the "FAST-9" corner detection algorithm explained in the paper 'FASTER and better: A machine learning approach to corner detection' by Rosten E., Porter R. and Drummond T. (2008), available at <arXiv:0810.2434>. The package allows to detect corners in digital images.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp

59.4 match 279 stars 5.14 score 7 scripts

bnosac

image.Otsu:Otsu's Image Segmentation Method

An implementation of the Otsu's Image Segmentation Method described in the paper: "A C++ Implementation of Otsu's Image Segmentation Method". The algorithm is explained at <doi:10.5201/ipol.2016.158>.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp

58.3 match 279 stars 5.14 score

cloudyr

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 1 days ago.

api cloud-computing cloudyr google-cloud googleauthr launching-virtual-machines

30.0 match 152 stars 9.73 score 235 scripts

bnosac

image.libfacedetection:Convolutional Neural Network for Face Detection

An open source library for face detection in images. Provides a pretrained convolutional neural network based on <https://github.com/ShiqiYu/libfacedetection> which can be used to detect faces which have size greater than 10x10 pixels.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp openmp

54.8 match 279 stars 5.29 score 14 scripts

bnosac

image.CornerDetectionHarris:Implementation of the Harris Corner Detection for Images

An implementation of the Harris Corner Detection as described in the paper "An Analysis and Implementation of the Harris Corner Detector" by Sánchez J. et al (2018) available at <doi:10.5201/ipol.2018.229>. The package allows to detect relevant points in images which are characteristic to the digital image.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp openmp

56.3 match 279 stars 5.14 score 2 scripts

eagerai

fastai:Interface to 'fastai'

The 'fastai' <https://docs.fast.ai/index.html> library simplifies training fast and accurate neural networks using modern best practices. It is based on research in to deep learning best practices undertaken at 'fast.ai', including 'out of the box' support for vision, text, tabular, audio, time series, and collaborative filtering models.

Maintained by Turgut Abdullayev. Last updated 11 months ago.

audio collaborative-filtering darknet darknet-image-classification fastai medical object-detection tabular text vision

30.6 match 118 stars 9.40 score 76 scripts

gtatters

Thermimage:Thermal Image Analysis

A collection of functions and routines for inputting thermal image video files, plotting and converting binary raw data into estimates of temperature. First published 2015-03-26. Written primarily for research purposes in biological applications of thermal images. v1 included the base calculations for converting thermal image binary values to temperatures. v2 included additional equations for providing heat transfer calculations and an import function for thermal image files (v2.2.3 fixed error importing thermal image to windows OS). v3. Added numerous functions for converting thermal image, videos, rewriting and exporting. v3.1. Added new functions to convert files. v3.2. Fixed the various functions related to finding frame times. v4.0. fixed an error in atmospheric attenuation constants, affecting raw2temp and temp2raw functions. Recommend update for use with long distance calculations. v.4.1.3. changed to frameLocates to reflect change to as.character() to format().

Maintained by Glenn J. Tattersall. Last updated 3 years ago.

animal-physiology heat-exchange heat-flux image-frames temperature thermal-biology thermal-images

48.0 match 169 stars 5.85 score 83 scripts

e-sensing

sits:Satellite Image Time Series Analysis for Earth Observation Data Cubes

An end-to-end toolkit for land use and land cover classification using big Earth observation data, based on machine learning methods applied to satellite image data cubes, as described in Simoes et al (2021) <doi:10.3390/rs13132428>. Builds regular data cubes from collections in AWS, Microsoft Planetary Computer, Brazil Data Cube, Copernicus Data Space Environment (CDSE), Digital Earth Africa, Digital Earth Australia, NASA HLS using the Spatio-temporal Asset Catalog (STAC) protocol (<https://stacspec.org/>) and the 'gdalcubes' R package developed by Appel and Pebesma (2019) <doi:10.3390/data4030092>. Supports visualization methods for images and time series and smoothing filters for dealing with noisy time series. Includes functions for quality assessment of training samples using self-organized maps as presented by Santos et al (2021) <doi:10.1016/j.isprsjprs.2021.04.014>. Includes methods to reduce training samples imbalance proposed by Chawla et al (2002) <doi:10.1613/jair.953>. Provides machine learning methods including support vector machines, random forests, extreme gradient boosting, multi-layer perceptrons, temporal convolutional neural networks proposed by Pelletier et al (2019) <doi:10.3390/rs11050523>, and temporal attention encoders by Garnot and Landrieu (2020) <doi:10.48550/arXiv.2007.00586>. Supports GPU processing of deep learning models using torch <https://torch.mlverse.org/>. Performs efficient classification of big Earth observation data cubes and includes functions for post-classification smoothing based on Bayesian inference as described by Camara et al (2024) <doi:10.3390/rs16234572>, and methods for active learning and uncertainty assessment. Supports region-based time series analysis using package supercells <https://jakubnowosad.com/supercells/>. Enables best practices for estimating area and assessing accuracy of land change as recommended by Olofsson et al (2014) <doi:10.1016/j.rse.2014.02.015>. Minimum recommended requirements: 16 GB RAM and 4 CPU dual-core.

Maintained by Gilberto Camara. Last updated 1 months ago.

big-earth-data cbers earth-observation eo-datacubes geospatial image-time-series land-cover-classification landsat planetary-computer r-spatial remote-sensing rspatial satellite-image-time-series satellite-imagery sentinel-2 stac-api stac-catalog cpp

28.0 match 494 stars 9.50 score 384 scripts

stevenvb12

patternize:Quantification of Color Pattern Variation

Quantification of variation in organismal color patterns as obtained from image data. Patternize defines homology between pattern positions across images either through fixed landmarks or image registration. Pattern identification is performed by categorizing the distribution of colors using RGB thresholds or image segmentation.

Maintained by Steven Van Belleghem. Last updated 9 months ago.

52.8 match 31 stars 4.97 score 30 scripts

opengeos

whitebox:'WhiteboxTools' R Frontend

An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. Suggested citation: Lindsay (2016) <doi:10.1016/j.cageo.2016.07.003>.

Maintained by Andrew Brown. Last updated 5 months ago.

geomorphometry geoprocessing geospatial gis hydrology remote-sensing rstudio

26.6 match 173 stars 9.65 score 203 scripts 2 dependents

piplus2

SPUTNIK:Spatially Automatic Denoising for Imaging Mass Spectrometry Toolkit

Set of tools for peak filtering of mass spectrometry imaging data based on spatial distribution of signal. Given a region-of-interest, representing the spatial region where the informative signal is expected to be localized, a series of filters determine which peak signals are characterized by an implausible spatial distribution. The filters reduce the dataset dimension and increase its information vs noise ratio, improving the quality of the unsupervised analysis results, reducing data dimension and simplifying the chemical interpretation. The methods are described in Inglese P. et al (2019) <doi:10.1093/bioinformatics/bty622>.

Maintained by Paolo Inglese. Last updated 11 months ago.

bioinformatics desi-msi image-processing maldi-msi maldi-tof-ms mass-spectrometry mass-spectrometry-imaging

48.2 match 4 stars 5.24 score 43 scripts

kangy10

DRIP:Discontinuous Regression and Image Processing

A collection of functions that perform jump regression and image analysis such as denoising, deblurring and jump detection. The implemented methods are based on the following research: Qiu, P. (1998) <doi:10.1214/aos/1024691468>, Qiu, P. and Yandell, B. (1997) <doi: 10.1080/10618600.1997.10474746>, Qiu, P. (2009) <doi: 10.1007/s10463-007-0166-9>, Kang, Y. and Qiu, P. (2014) <doi: 10.1080/00401706.2013.844732>, Qiu, P. and Kang, Y. (2015) <doi: 10.5705/ss.2014.054>, Kang, Y., Mukherjee, P.S. and Qiu, P. (2018) <doi: 10.1080/00401706.2017.1415975>, Kang, Y. (2020) <doi: 10.1080/10618600.2019.1665536>.

Maintained by Yicheng Kang. Last updated 4 months ago.

fortran openblas

45.4 match 5.49 score 31 scripts

appelmar

gdalcubes:Earth Observation Data Cubes from Satellite Image Collections

Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time, applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values, exporting data cubes as 'netCDF' or 'GeoTIFF' files, plotting, and extraction from spatial and or spatiotemporal features. All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries. See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.

Maintained by Marius Appel. Last updated 1 years ago.

remote-sensing satellite-imagery spatial-analysis gdal netcdf cpp

29.6 match 124 stars 8.39 score 356 scripts

bioc

SPIAT:Spatial Image Analysis of Tissues

SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.

Maintained by Yuzhou Feng. Last updated 18 hours ago.

biomedicalinformatics cellbiology spatial clustering dataimport immunooncology qualitycontrol singlecell software visualization

28.6 match 22 stars 8.59 score 69 scripts

mbeauvai

AFM:Atomic Force Microscope Image Analysis

Provides Atomic Force Microscope images analysis such as Gaussian mixes identification, Power Spectral Density, roughness against lengthscale, experimental variogram and variogram models, fractal dimension and scale, 2D network analysis. The AFM images can be exported to STL format for 3D printing.

Maintained by Mathieu Beauvais. Last updated 4 years ago.

81.4 match 1 stars 2.96 score 92 scripts

trevorld

ggpattern:'ggplot2' Pattern Geoms

Provides 'ggplot2' geoms filled with various patterns. Includes a patterned version of every 'ggplot2' geom that has a region that can be filled with a pattern. Provides a suite of 'ggplot2' aesthetics and scales for controlling pattern appearances. Supports over a dozen builtin patterns (every pattern implemented by 'gridpattern') as well as allowing custom user-defined patterns.

Maintained by Trevor L. Davis. Last updated 2 months ago.

19.4 match 368 stars 12.33 score 1.7k scripts 3 dependents

coolbutuseless

nara:Native Raster Image Tools

Tools for 'nativeRaster' images.

Maintained by Mike Cheng. Last updated 29 days ago.

gfx graphics pkg

37.4 match 62 stars 6.32 score 42 scripts

cran

ExpImage:Analysis of Images in Experiments

Tools created for image analysis in researches. There are functions associated with image editing, segmentation, and obtaining biometric measurements (Este pacote foi idealizado para para a analise de imagens em pesquisas. Ha funcoes associadas a edicao de imagens, segmentacao, e obtencao de medidas biometricas) <https://www.expstat.com/pacotes-do-r/expimage>.

Maintained by Alcinei Mistico Azevedo. Last updated 10 months ago.

74.5 match 3.08 score

bioc

RBioFormats:R interface to Bio-Formats

An R package which interfaces the OME Bio-Formats Java library to allow reading of proprietary microscopy image data and metadata.

Maintained by Andrzej Oleś. Last updated 5 months ago.

dataimport bio-formats bioconductor image-processing openjdk

29.3 match 25 stars 7.74 score 82 scripts 1 dependents

satijalab

Seurat:Tools for Single Cell Genomics

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

Maintained by Paul Hoffman. Last updated 1 years ago.

human-cell-atlas single-cell-genomics single-cell-rna-seq cpp

13.2 match 2.4k stars 16.86 score 50k scripts 73 dependents

europeanifcbgroup

iRfcb:Tools for Managing Imaging FlowCytobot (IFCB) Data

A comprehensive suite of tools for managing, processing, and analyzing data from the IFCB. I R FlowCytobot ('iRfcb') supports quality control, geospatial analysis, and preparation of IFCB data for publication in databases like <https://www.gbif.org>, <https://www.obis.org>, <https://emodnet.ec.europa.eu/en>, <https://shark.smhi.se/>, and <https://www.ecotaxa.org>. The package integrates with the MATLAB 'ifcb-analysis' tool, which is described in Sosik and Olson (2007) <doi:10.4319/lom.2007.5.204>, and provides features for working with raw, manually classified, and machine learning–classified image datasets. Key functionalities include image extraction, particle size distribution analysis, taxonomic data handling, and biomass concentration calculations, essential for plankton research.

Maintained by Anders Torstensson. Last updated 15 hours ago.

38.7 match 1 stars 5.72 score

jonclayden

RNifti:Fast R and C++ Access to NIfTI Images

Provides very fast read and write access to images stored in the NIfTI-1, NIfTI-2 and ANALYZE-7.5 formats, with seamless synchronisation of in-memory image objects between compiled C and interpreted R code. Also provides a simple image viewer, and a C/C++ API that can be used by other packages. Not to be confused with 'RNiftyReg', which performs image registration and applies spatial transformations.

Maintained by Jon Clayden. Last updated 23 days ago.

medical-imaging nifti-format zlib cpp

21.2 match 48 stars 10.43 score 522 scripts 56 dependents

gitdemont

IFC:Tools for Imaging Flow Cytometry

Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®' 'Cytek®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata/>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.

Maintained by Yohann Demont. Last updated 10 days ago.

cytometry cytometry-data flow flow-cytometry flow-cytometry-analysis flow-cytometry-data flow-cytometry-files ifc image imaging-flow-cytometry imaging-flow-cytometry-data microscopy cpp

41.0 match 4 stars 5.34 score 12 scripts

shotaochi

imagerExtra:Extra Image Processing Library Based on 'imager'

Provides advanced functions for image processing based on the package 'imager'.

Maintained by Shota Ochi. Last updated 2 years ago.

image-processing imager cpp

42.0 match 11 stars 5.22 score

tylermorganwall

rayimage:Image Processing for Simulated Cameras

Uses convolution-based techniques to generate simulated camera bokeh, depth of field, and other camera effects, using an image and an optional depth map. Accepts both filename inputs and in-memory array representations of images and matrices. Includes functions to perform 2D convolutions, reorient and resize images/matrices, add image and text overlays, generate camera vignette effects, and add titles to images.

Maintained by Tyler Morgan-Wall. Last updated 1 months ago.

cpp

28.2 match 52 stars 7.67 score 22 scripts 12 dependents

spatstat

spatstat.linnet:Linear Networks Functionality of the 'spatstat' Family

Defines types of spatial data on a linear network and provides functionality for geometrical operations, data analysis and modelling of data on a linear network, in the 'spatstat' family of packages. Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks. Data types defined on a network include point patterns, pixel images, functions, and tessellations. Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported. Parametric models can be fitted to point pattern data using the function lppm() similar to glm(). Only Poisson models are implemented so far. Models may involve dependence on covariates and dependence on marks. Models are fitted by maximum likelihood. Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots. Random point patterns on a network can be generated using a variety of models.

Maintained by Adrian Baddeley. Last updated 2 months ago.

density-estimation heat-equation kernel-density-estimation network-analysis point-processes spatial-data-analysis statistical-analysis statistical-inference statistical-models

22.1 match 6 stars 9.64 score 35 scripts 43 dependents

jonclayden

RNiftyReg:Image Registration Using the 'NiftyReg' Library

Provides an 'R' interface to the 'NiftyReg' image registration tools <https://github.com/KCL-BMEIS/niftyreg>. Linear and nonlinear registration are supported, in two and three dimensions.

Maintained by Jon Clayden. Last updated 6 months ago.

image-registration medical-imaging transformations cpp openmp

27.6 match 43 stars 7.64 score 50 scripts 5 dependents

cesarofs

agriwater:Evapotranspiration and Energy Fluxes Spatial Analysis

Spatial modeling of energy balance and actual evapotranspiration using satellite images and meteorological data. Options of satellite are: Landsat-8 (with and without thermal bands), Sentinel-2 and MODIS. Respectively spatial resolutions are 30, 100, 10 and 250 meters. User can use data from a single meteorological station or a grid of meteorological stations (using any spatial interpolation method). Silva, Teixeira, and Manzione (2019) <doi:10.1016/j.envsoft.2019.104497>.

Maintained by Cesar de Oliveira Ferreira Silva. Last updated 2 years ago.

40.5 match 9 stars 5.05 score 25 scripts

edzer

sp:Classes and Methods for Spatial Data

Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc. From this version, 'rgdal', 'maptools', and 'rgeos' are no longer used at all, see <https://r-spatial.org/r/2023/05/15/evolution4.html> for details.

Maintained by Edzer Pebesma. Last updated 2 months ago.

10.9 match 127 stars 18.63 score 35k scripts 1.3k dependents

dfsp-spirit

fsbrain:Managing and Visualizing Brain Surface Data

Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.

Maintained by Tim Schäfer. Last updated 4 months ago.

3d brain dti freesurfer mesh mri neuroimaging research surface visualization voxel

31.1 match 66 stars 6.47 score 15 scripts

brauckhoff

biopixR:Extracting Insights from Biological Images

Combines the 'magick' and 'imager' packages to streamline image analysis, focusing on feature extraction and quantification from biological images, especially microparticles. By providing high throughput pipelines and clustering capabilities, 'biopixR' facilitates efficient insight generation for researchers (Schneider J. et al. (2019) <doi:10.21037/jlpm.2019.04.05>).

Maintained by Tim Brauckhoff. Last updated 4 months ago.

31.5 match 5 stars 6.36 score 23 scripts

great-northern-diver

loon:Interactive Statistical Data Visualization

An extendable toolkit for interactive data visualization and exploration.

Maintained by R. Wayne Oldford. Last updated 2 years ago.

data-analysis data-science data-visualization exploratory-analysis exploratory-data-analysis high-dimensional-data interactive-graphics interactive-visualizations loon python statistical-analysis statistical-graphics statistics tcl-extension tk

22.2 match 48 stars 9.00 score 93 scripts 5 dependents

hiweller

colordistance:Distance Metrics for Image Color Similarity

Loads and displays images, selectively masks specified background colors, bins pixels by color using either data-dependent or automatically generated color bins, quantitatively measures color similarity among images using one of several distance metrics for comparing pixel color clusters, and clusters images by object color similarity. Uses CIELAB, RGB, or HSV color spaces. Originally written for use with organism coloration (reef fish color diversity, butterfly mimicry, etc), but easily applicable for any image set.

Maintained by Hannah Weller. Last updated 1 years ago.

24.3 match 37 stars 7.93 score 76 scripts 2 dependents

spatstat

spatstat.model:Parametric Statistical Modelling and Inference for the 'spatstat' Family

Functionality for parametric statistical modelling and inference for spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Supports parametric modelling, formal statistical inference, and model validation. Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope tests, Dao-Genton test, balanced independent two-stage test), confidence intervals for parameters, and prediction intervals for point counts. Model validation techniques include leverage, influence, partial residuals, added variable plots, diagnostic plots, pseudoscore residual plots, model compensators and Q-Q plots.

Maintained by Adrian Baddeley. Last updated 8 days ago.

analysis-of-variance cluster-process confidence-intervals cox-process determinantal-point-processes gibbs-process influence leverage model-diagnostics neyman-scott parameter-estimation poisson-process spatial-analysis spatial-modelling spatial-point-processes statistical-inference

20.3 match 5 stars 9.09 score 6 scripts 46 dependents

digi-vub

image.binarization:Binarize Images for Enhancing Optical Character Recognition

Improve optical character recognition by binarizing images. The package focuses primarily on local adaptive thresholding algorithms. In English, this means that it has the ability to turn a color or gray scale image into a black and white image. This is particularly useful as a preprocessing step for optical character recognition or handwritten text recognition.

Maintained by Jan Wijffels. Last updated 3 years ago.

cpp

43.1 match 21 stars 4.17 score 14 scripts

r-lum

Luminescence:Comprehensive Luminescence Dating Data Analysis

A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.

Maintained by Sebastian Kreutzer. Last updated 1 days ago.

bayesian-statistics data-science geochronology luminescence luminescence-dating open-science osl plotting radiofluorescence tl xsyg cpp

16.5 match 15 stars 10.77 score 178 scripts 8 dependents

stm

imagefluency:Image Statistics Based on Processing Fluency

Get image statistics based on processing fluency theory. The functions provide scores for several basic aesthetic principles that facilitate fluent cognitive processing of images: contrast, complexity / simplicity, self-similarity, symmetry, and typicality. See Mayer & Landwehr (2018) <doi:10.1037/aca0000187> and Mayer & Landwehr (2018) <doi:10.31219/osf.io/gtbhw> for the theoretical background of the methods.

Maintained by Stefan Mayer. Last updated 1 years ago.

fluency image-analysis image-analytics

35.0 match 10 stars 5.00 score 9 scripts

digi-vub

image.textlinedetector:Segment Images in Text Lines and Words

Find text lines in scanned images and segment the lines into words. Includes implementations of the paper 'Novel A* Path Planning Algorithm for Line Segmentation of Handwritten Documents' by Surinta O. et al (2014) <doi:10.1109/ICFHR.2014.37> available at <https://github.com/smeucci/LineSegm>, an implementation of 'A Statistical approach to line segmentation in handwritten documents' by Arivazhagan M. et al (2007) <doi:10.1117/12.704538>, and a wrapper for an image segmentation technique to detect words in text lines as described in the paper 'Scale Space Technique for Word Segmentation in Handwritten Documents' by Manmatha R. and Srimal N. (1999) paper at <doi:10.1007/3-540-48236-9_3>, wrapper for code available at <https://github.com/arthurflor23/text-segmentation>. Provides as well functionality to put cursive text in images upright using the approach defined in the paper 'A new normalization technique for cursive handwritten words' by Vinciarelli A. and Luettin J. (2001) <doi:10.1016/S0167-8655(01)00042-3>.

Maintained by Jan Wijffels. Last updated 10 days ago.

opencv cpp

44.9 match 8 stars 3.88 score 19 scripts

rorynolan

nandb:Number and Brightness Image Analysis

Calculation of molecular number and brightness from fluorescence microscopy image series. The software was published in a 2016 paper <doi:10.1093/bioinformatics/btx434>. The seminal paper for the technique is Digman et al. 2008 <doi:10.1529/biophysj.107.114645>. A review of the technique was published in 2017 <doi:10.1016/j.ymeth.2017.12.001>.

Maintained by Rory Nolan. Last updated 2 months ago.

cpp

32.9 match 2 stars 5.24 score 29 scripts

cloudyr

imguR:'Imgur.com' API Client Package

A complete API client for the image hosting service 'Imgur.com', including the an 'imgur' graphics device, enabling the easy upload and sharing of plots.

Maintained by Thomas J. Leeper. Last updated 7 years ago.

cloudyr imgur

29.4 match 16 stars 5.82 score 46 scripts 6 dependents

gzt

catsim:Binary and Categorical Image Similarity Index

Computes a structural similarity metric (after the style of MS-SSIM for images) for binary and categorical 2D and 3D images. Can be based on accuracy (simple matching), Cohen's kappa, Rand index, adjusted Rand index, Jaccard index, Dice index, normalized mutual information, or adjusted mutual information. In addition, has fast computation of Cohen's kappa, the Rand indices, and the two mutual informations. Implements the methods of Thompson and Maitra (2020) <doi:10.48550/arXiv.2004.09073>.

Maintained by Geoffrey Thompson. Last updated 6 months ago.

binary-data binary-image-classification binary-image-processing categorical-data categorical-images classification image-processing cpp

38.8 match 5 stars 4.40 score 5 scripts

pachadotdev

analogsea:Interface to 'DigitalOcean'

Provides a set of functions for interacting with the 'DigitalOcean' API <https://www.digitalocean.com/>, including creating images, destroying them, rebooting, getting details on regions, and available images.

Maintained by Mauricio Vargas. Last updated 2 years ago.

cloud-computing droplet ssh

22.2 match 159 stars 7.56 score 100 scripts 1 dependents

ropensci

rsat:Dealing with Multiplatform Satellite Images

Downloading, customizing, and processing time series of satellite images for a region of interest. 'rsat' functions allow a unified access to multispectral images from Landsat, MODIS and Sentinel repositories. 'rsat' also offers capabilities for customizing satellite images, such as tile mosaicking, image cropping and new variables computation. Finally, 'rsat' covers the processing, including cloud masking, compositing and gap-filling/smoothing time series of images (Militino et al., 2018 <doi:10.3390/rs10030398> and Militino et al., 2019 <doi:10.1109/TGRS.2019.2904193>).

Maintained by Unai Pérez - Goya. Last updated 11 months ago.

satellite-images

22.1 match 54 stars 7.45 score 52 scripts

jiefei-wang

aws.ecx:Communicating with AWS EC2 and ECS using AWS REST APIs

Providing the functions for communicating with Amazon Web Services(AWS) Elastic Compute Cloud(EC2) and Elastic Container Service(ECS). The functions will have the prefix 'ecs_' or 'ec2_' depending on the class of the API. The request will be sent via the REST API and the parameters are given by the function argument. The credentials can be set via 'aws_set_credentials'. The EC2 documentation can be found at <https://docs.aws.amazon.com/AWSEC2/latest/APIReference/Welcome.html> and ECS can be found at <https://docs.aws.amazon.com/AmazonECS/latest/APIReference/Welcome.html>.

Maintained by Jiefei Wang. Last updated 3 years ago.

ec2 ecs ecs-functions

39.1 match 1 stars 4.18 score 2 scripts

pamelarussell

TCIApathfinder:Client for the Cancer Imaging Archive REST API

A wrapper for The Cancer Imaging Archive's REST API. The Cancer Imaging Archive (TCIA) hosts de-identified medical images of cancer available for public download, as well as rich metadata for each image series. TCIA provides a REST API for programmatic access to the data. This package provides simple functions to access each API endpoint. For more information, see <https://github.com/pamelarussell/TCIApathfinder> and TCIA's website.

Maintained by Pamela Russell. Last updated 4 years ago.

tcia-dac

28.4 match 9 stars 5.70 score 28 scripts

r-spatial

stars:Spatiotemporal Arrays, Raster and Vector Data Cubes

Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.

Maintained by Edzer Pebesma. Last updated 30 days ago.

raster satellite-images spatial

8.8 match 571 stars 18.27 score 7.2k scripts 137 dependents

bleutner

RStoolbox:Remote Sensing Data Analysis

Toolbox for remote sensing image processing and analysis such as calculating spectral indexes, principal component transformation, unsupervised and supervised classification or fractional cover analyses.

Maintained by Konstantin Mueller. Last updated 1 months ago.

ggplot2 land-cover-mapping remote-sensing spectral-unmixing supervised-classification unsupervised-classification openblas cpp

15.9 match 275 stars 10.10 score 1.1k scripts

michaelhallquist

ggbrain:Create Images of Volumetric Brain Data in NIfTI Format Using 'ggplot2' Syntax

A 'ggplot2'-consistent approach to generating 2D displays of volumetric brain imaging data. Display data from multiple NIfTI images using standard 'ggplot2' conventions such scales, limits, and themes to control the appearance of displays. The resulting plots are returned as 'patchwork' objects, inheriting from 'ggplot', allowing for any standard modifications of display aesthetics supported by 'ggplot2'.

Maintained by Michael Hallquist. Last updated 25 days ago.

cpp

31.5 match 2 stars 5.03 score 18 scripts

rstudio

gt:Easily Create Presentation-Ready Display Tables

Build display tables from tabular data with an easy-to-use set of functions. With its progressive approach, we can construct display tables with a cohesive set of table parts. Table values can be formatted using any of the included formatting functions. Footnotes and cell styles can be precisely added through a location targeting system. The way in which 'gt' handles things for you means that you don't often have to worry about the fine details.

Maintained by Richard Iannone. Last updated 11 days ago.

docx easy-to-use html latex rtf summary-tables

8.5 match 2.1k stars 18.36 score 20k scripts 112 dependents

guangchuangyu

ggimage:Use Image in 'ggplot2'

Supports image files and graphic objects to be visualized in 'ggplot2' graphic system.

Maintained by Guangchuang Yu. Last updated 1 years ago.

ggplot2 image visualization

13.9 match 172 stars 11.16 score 2.4k scripts 20 dependents

oobianom

quickcode:Quick and Essential 'R' Tricks for Better Scripts

The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to improve your scripts. Improve the quality and reproducibility of 'R' scripts.

Maintained by Obinna Obianom. Last updated 14 days ago.

colors data distributions images

19.6 match 5 stars 7.76 score 7 scripts 6 dependents

palaeoverse

rphylopic:Get Silhouettes of Organisms from PhyloPic

Work with the PhyloPic Web Service (<http://api-docs.phylopic.org/v2/>) to fetch silhouette images of organisms. Includes functions for adding silhouettes to both base R plots and ggplot2 plots.

Maintained by William Gearty. Last updated 6 months ago.

base-r ggplot2 phylopic silhouette

15.6 match 91 stars 9.25 score 272 scripts

muschellij2

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.

Maintained by John Muschelli. Last updated 10 months ago.

23.1 match 9 stars 6.22 score 61 scripts

martin3141

spant:MR Spectroscopy Analysis Tools

Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.

Maintained by Martin Wilson. Last updated 30 days ago.

brain mri mrs mrshub spectroscopy fortran

16.8 match 25 stars 8.52 score 81 scripts

rapporter

pander:An R 'Pandoc' Writer

Contains some functions catching all messages, 'stdout' and other useful information while evaluating R code and other helpers to return user specified text elements (like: header, paragraph, table, image, lists etc.) in 'pandoc' markdown or several type of R objects similarly automatically transformed to markdown format. Also capable of exporting/converting (the resulting) complex 'pandoc' documents to e.g. HTML, 'PDF', 'docx' or 'odt'. This latter reporting feature is supported in brew syntax or with a custom reference class with a smarty caching 'backend'.

Maintained by Gergely Daróczi. Last updated 16 days ago.

literate-programming markdown pandoc pandoc-markdown reproducible-research rmarkdown cpp

8.5 match 297 stars 16.60 score 7.6k scripts 108 dependents

mjlajeunesse

metagear:Comprehensive Research Synthesis Tools for Systematic Reviews and Meta-Analysis

Functionalities for facilitating systematic reviews, data extractions, and meta-analyses. It includes a GUI (graphical user interface) to help screen the abstracts and titles of bibliographic data; tools to assign screening effort across multiple collaborators/reviewers and to assess inter- reviewer reliability; tools to help automate the download and retrieval of journal PDF articles from online databases; figure and image extractions from PDFs; web scraping of citations; automated and manual data extraction from scatter-plot and bar-plot images; PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) flow diagrams; simple imputation tools to fill gaps in incomplete or missing study parameters; generation of random effects sizes for Hedges' d, log response ratio, odds ratio, and correlation coefficients for Monte Carlo experiments; covariance equations for modelling dependencies among multiple effect sizes (e.g., effect sizes with a common control); and finally summaries that replicate analyses and outputs from widely used but no longer updated meta-analysis software (i.e., metawin). Funding for this package was supported by National Science Foundation (NSF) grants DBI-1262545 and DEB-1451031. CITE: Lajeunesse, M.J. (2016) Facilitating systematic reviews, data extraction and meta-analysis with the metagear package for R. Methods in Ecology and Evolution 7, 323-330 <doi:10.1111/2041-210X.12472>.

Maintained by Marc J. Lajeunesse. Last updated 4 years ago.

21.0 match 14 stars 6.71 score 91 scripts

spatstat

spatstat.explore:Exploratory Data Analysis for the 'spatstat' Family

Functionality for exploratory data analysis and nonparametric analysis of spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.

Maintained by Adrian Baddeley. Last updated 1 months ago.

cluster-detection confidence-intervals hypothesis-testing k-function roc-curves scan-statistics significance-testing simulation-envelopes spatial-analysis spatial-data-analysis spatial-sharpening spatial-smoothing spatial-statistics

13.8 match 1 stars 10.17 score 67 scripts 148 dependents

bioc

cytoviewer:An interactive multi-channel image viewer for R

This R package supports interactive visualization of multi-channel images and segmentation masks generated by imaging mass cytometry and other highly multiplexed imaging techniques using shiny. The cytoviewer interface is divided into image-level (Composite and Channels) and cell-level visualization (Masks). It allows users to overlay individual images with segmentation masks, integrates well with SingleCellExperiment and SpatialExperiment objects for metadata visualization and supports image downloads.

Maintained by Lasse Meyer. Last updated 5 months ago.

immunooncology software singlecell onechannel twochannel multichannel spatial dataimport bioconductor imaging shiny visualization

25.3 match 7 stars 5.50 score 15 scripts

cran

adimpro:Adaptive Smoothing of Digital Images

Implements tools for manipulation of digital images and the Propagation Separation approach by Polzehl and Spokoiny (2006) <DOI:10.1007/s00440-005-0464-1> for smoothing digital images, see Polzehl and Tabelow (2007) <DOI:10.18637/jss.v019.i01>.

Maintained by Karsten Tabelow. Last updated 6 months ago.

fortran openblas openmp

52.1 match 2.66 score 38 scripts 2 dependents

alexjcwitsil

imagefx:Extract Features from Images

Synthesize images into characteristic features for time-series analysis or machine learning applications. The package was originally intended for monitoring volcanic eruptions in video data by highlighting and extracting regions above the vent associated with plume activity. However, the functions within are general and have wide applications for image processing, analyzing, filtering, and plotting.

Maintained by Alex J.C. Witsil. Last updated 5 years ago.

59.1 match 2.34 score 11 scripts

bioc

SpatialOmicsOverlay:Spatial Overlay for Omic Data from Nanostring GeoMx Data

Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression.

Maintained by Maddy Griswold. Last updated 5 months ago.

geneexpression transcription cellbasedassays dataimport transcriptomics proteomics proprietaryplatforms rnaseq spatial datarepresentation visualization openjdk

32.0 match 4.30 score 8 scripts

dfsp-spirit

wal:Read and Write 'wal' Bitmap Image Files and Other 'Quake' Assets

Read 'Quake' assets including bitmap images and textures in 'wal' file format. This package also provides support for extracting these assets from 'WAD' and 'PAK' file archives. It can also read models in 'MDL' and 'MD2' formats.

Maintained by Tim Schäfer. Last updated 1 years ago.

image pak quake quake-engine quake2 textures wad wal

29.2 match 9 stars 4.65 score 1 scripts

satijalab

SeuratObject:Data Structures for Single Cell Data

Defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. Provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.

Maintained by Paul Hoffman. Last updated 1 years ago.

cpp

11.6 match 25 stars 11.69 score 1.2k scripts 88 dependents

brownag

rgeedim:Search, Composite, and Download 'Google Earth Engine' Imagery with the 'Python' Module 'geedim'

Search, composite, and download 'Google Earth Engine' imagery with 'reticulate' bindings for the 'Python' module 'geedim' by Dugal Harris. Read the 'geedim' documentation here: <https://geedim.readthedocs.io/>. Wrapper functions are provided to make it more convenient to use 'geedim' to download images larger than the 'Google Earth Engine' size limit <https://developers.google.com/earth-engine/apidocs/ee-image-getdownloadurl>. By default the "High Volume" API endpoint <https://developers.google.com/earth-engine/cloud/highvolume> is used to download data and this URL can be customized during initialization of the package.

Maintained by Andrew Brown. Last updated 24 days ago.

geedim geotiff gis google-earth-engine python raster remote-sensing satellite-imagery spatial terra

22.1 match 48 stars 5.81 score 27 scripts

yihui

knitr:A General-Purpose Package for Dynamic Report Generation in R

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

Maintained by Yihui Xie. Last updated 4 hours ago.

dynamic-documents knitr literate-programming rmarkdown sweave

5.4 match 2.4k stars 23.61 score 116k scripts 4.2k dependents

rmaia

pavo:Perceptual Analysis, Visualization and Organization of Spectral Colour Data

A cohesive framework for the spectral and spatial analysis of colour described in Maia, Eliason, Bitton, Doucet & Shawkey (2013) <doi:10.1111/2041-210X.12069> and Maia, Gruson, Endler & White (2019) <doi:10.1111/2041-210X.13174>.

Maintained by Thomas White. Last updated 1 months ago.

12.9 match 72 stars 9.72 score 151 scripts 1 dependents

dschuhmacher

transport:Computation of Optimal Transport Plans and Wasserstein Distances

Solve optimal transport problems. Compute Wasserstein distances (a.k.a. Kantorovitch, Fortet--Mourier, Mallows, Earth Mover's, or minimal L_p distances), return the corresponding transference plans, and display them graphically. Objects that can be compared include grey-scale images, (weighted) point patterns, and mass vectors.

Maintained by Dominic Schuhmacher. Last updated 6 months ago.

cpp openmp

15.1 match 5 stars 8.07 score 414 scripts 22 dependents

jthomasmock

gtExtras:Extending 'gt' for Beautiful HTML Tables

Provides additional functions for creating beautiful tables with 'gt'. The functions are generally wrappers around boilerplate or adding opinionated niche capabilities and helpers functions.

Maintained by Thomas Mock. Last updated 12 months ago.

data-science data-visualization datascience ggplot2 gt plots sparkline sparkline-graphs sparklines tables

10.6 match 199 stars 11.45 score 2.4k scripts 3 dependents

rstudio

shiny:Web Application Framework for R

Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.

Maintained by Winston Chang. Last updated 13 days ago.

reactive rstudio shiny web-app web-development

5.7 match 5.4k stars 21.28 score 108k scripts 1.8k dependents

haozhu233

kableExtra:Construct Complex Table with 'kable' and Pipe Syntax

Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and the piping syntax from 'magrittr'. Function 'kable()' is a light weight table generator coming from 'knitr'. This package simplifies the way to manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct complex tables and customize styles using a readable syntax.

Maintained by Hao Zhu. Last updated 10 days ago.

html kable kableextra knitr latex rmarkdown

6.2 match 702 stars 19.35 score 55k scripts 163 dependents

tractor

tractor.base:Read, Manipulate and Visualise Magnetic Resonance Images

Functions for working with magnetic resonance images. Reading and writing of popular file formats (DICOM, Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive visualisation; flexible image manipulation; metadata and sparse image handling.

Maintained by Jon Clayden. Last updated 2 hours ago.

brain-imaging graph-algorithms parcellation tractography

17.3 match 28 stars 6.79 score 35 scripts 1 dependents

bioc

RCy3:Functions to Access and Control Cytoscape

Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.

Maintained by Alex Pico. Last updated 5 months ago.

visualization graphandnetwork thirdpartyclient network

8.7 match 52 stars 13.39 score 628 scripts 15 dependents

rorynolan

autothresholdr:An R Port of the 'ImageJ' Plugin 'Auto Threshold'

Algorithms for automatically finding appropriate thresholds for numerical data, with special functions for thresholding images. Provides the 'ImageJ' 'Auto Threshold' plugin functionality to R users. See <https://imagej.net/plugins/auto-threshold> and Landini et al. (2017) <DOI:10.1111/jmi.12474>.

Maintained by Rory Nolan. Last updated 1 years ago.

cpp

17.0 match 6 stars 6.73 score 31 scripts 4 dependents

leonawicz

imgpalr:Create Color Palettes from Images

Provides ability to create color palettes from image files. It offers control over the type of color palette to derive from an image (qualitative, sequential or divergent) and other palette properties. Quantiles of an image color distribution can be trimmed. Near-black or near-white colors can be trimmed in RGB color space independent of trimming brightness or saturation distributions in HSV color space. Creating sequential palettes also offers control over the order of HSV color dimensions to sort by. This package differs from other related packages like 'RImagePalette' in approaches to quantizing and extracting colors in images to assemble color palettes and the level of user control over palettes construction.

Maintained by Matthew Leonawicz. Last updated 6 months ago.

color color-palette image-classification image-processing

24.5 match 52 stars 4.65 score 17 scripts

bjw34032

waveslim:Basic Wavelet Routines for One-, Two-, and Three-Dimensional Signal Processing

Basic wavelet routines for time series (1D), image (2D) and array (3D) analysis. The code provided here is based on wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002). All figures in chapters 4-7 of GSW (2001) are reproducible using this package and R code available at the book website(s) below.

Maintained by Brandon Whitcher. Last updated 10 months ago.

wavelets

14.2 match 3 stars 7.88 score 108 scripts 23 dependents

marce10

warbleR:Streamline Bioacoustic Analysis

Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the packages 'tuneR' and 'seewave', and offers new tools for explore and quantify acoustic signal structure. The package allows to organize and manipulate multiple sound files, create spectrograms of complete recordings or individual signals in different formats, run several measures of acoustic structure, and characterize different structural levels in acoustic signals.

Maintained by Marcelo Araya-Salas. Last updated 2 months ago.

animal-acoustic-signals audio-processing bioacoustics spectrogram streamline-analysis cpp

10.1 match 54 stars 11.01 score 270 scripts 4 dependents

ecodynizw

imageseg:Deep Learning Models for Image Segmentation

A general-purpose workflow for image segmentation using TensorFlow models based on the U-Net architecture by Ronneberger et al. (2015) <arXiv:1505.04597> and the U-Net++ architecture by Zhou et al. (2018) <arXiv:1807.10165>. We provide pre-trained models for assessing canopy density and understory vegetation density from vegetation photos. In addition, the package provides a workflow for easily creating model input and model architectures for general-purpose image segmentation based on grayscale or color images, both for binary and multi-class image segmentation.

Maintained by Juergen Niedballa. Last updated 1 years ago.

image-segmentation keras tensorflow

22.4 match 18 stars 4.95 score 9 scripts

plotly

plotly:Create Interactive Web Graphics via 'plotly.js'

Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.

Maintained by Carson Sievert. Last updated 3 months ago.

d3js data-visualization ggplot2 javascript plotly shiny webgl

5.7 match 2.6k stars 19.43 score 93k scripts 797 dependents

bioc

spaSim:Spatial point data simulator for tissue images

A suite of functions for simulating spatial patterns of cells in tissue images. Output images are multitype point data in SingleCellExperiment format. Each point represents a cell, with its 2D locations and cell type. Potential cell patterns include background cells, tumour/immune cell clusters, immune rings, and blood/lymphatic vessels.

Maintained by Yuzhou Feng. Last updated 5 months ago.

statisticalmethod spatial biomedicalinformatics

21.2 match 2 stars 5.18 score 25 scripts

dieghernan

resmush:Optimize and Compress Image Files with 'reSmush.it'

Compress local and online images using the 'reSmush.it' API service <https://resmush.it/>.

Maintained by Diego Hernangómez. Last updated 1 months ago.

compress-images optimize-images resmushit api

18.5 match 2 stars 5.85 score 14 scripts 1 dependents

azure

azuremlsdk:Interface to the 'Azure Machine Learning' 'SDK'

Interface to the 'Azure Machine Learning' Software Development Kit ('SDK'). Data scientists can use the 'SDK' to train, deploy, automate, and manage machine learning models on the 'Azure Machine Learning' service. To learn more about 'Azure Machine Learning' visit the website: <https://docs.microsoft.com/en-us/azure/machine-learning/service/overview-what-is-azure-ml>.

Maintained by Diondra Peck. Last updated 3 years ago.

amlcompute azure azure-machine-learning azureml dsi machine-learning rstudio sdk-r

11.7 match 106 stars 8.91 score 221 scripts

rorynolan

detrendr:Detrend Images

Detrend fluorescence microscopy image series for fluorescence fluctuation and correlation spectroscopy ('FCS' and 'FFS') analysis. This package contains functionality published in a 2016 paper <doi:10.1093/bioinformatics/btx434> but it has been extended since then with the Robin Hood algorithm and thus contains unpublished work.

Maintained by Rory Nolan. Last updated 2 months ago.

cpp

16.9 match 3 stars 6.08 score 25 scripts 1 dependents

parklab

Nozzle.R1:Nozzle Reports

The Nozzle package provides an API to generate HTML reports with dynamic user interface elements based on JavaScript and CSS (Cascading Style Sheets). Nozzle was designed to facilitate summarization and rapid browsing of complex results in data analysis pipelines where multiple analyses are performed frequently on big data sets. The package can be applied to any project where user-friendly reports need to be created.

Maintained by Nils Gehlenborg. Last updated 10 years ago.

gehlenborglab html-report reproducible-research

19.3 match 68 stars 5.31 score 10 scripts 2 dependents

rspatial

raster:Geographic Data Analysis and Modeling

Reading, writing, manipulating, analyzing and modeling of spatial data. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.

Maintained by Robert J. Hijmans. Last updated 2 months ago.

cpp

6.0 match 164 stars 17.05 score 58k scripts 555 dependents

sysbiolab

PathwaySpace:Spatial Projection of Network Signals along Geodesic Paths

For a given graph containing vertices, edges, and a signal associated with the vertices, the 'PathwaySpace' package performs a convolution operation, which involves a weighted combination of neighboring vertices and their associated signals. The package then uses a decay function to project these signals, creating geodesic paths on a 2D-image space. 'PathwaySpace' could have various applications, such as visualizing and analyzing network data in a graphical format that highlights the relationships and signal strengths between vertices. It can be particularly useful for understanding the influence of signals through complex networks. By combining graph theory, signal processing, and visualization, the 'PathwaySpace' package provides a novel way of representing and analyzing graph data.

Maintained by Mauro Castro. Last updated 2 months ago.

bioinformatics biological-networks graph

20.9 match 2 stars 4.85 score 5 scripts

ropensci

colocr:Conduct Co-Localization Analysis of Fluorescence Microscopy Images

Automate the co-localization analysis of fluorescence microscopy images. Selecting regions of interest, extract pixel intensities from the image channels and calculate different co-localization statistics. The methods implemented in this package are based on Dunn et al. (2011) <doi:10.1152/ajpcell.00462.2010>.

Maintained by Mahmoud Ahmed. Last updated 5 years ago.

colocalization image-analysis

17.4 match 26 stars 5.76 score 22 scripts

bioimaginggroup

bioimagetools:Tools for Microscopy Imaging

Tools for 3D imaging, mostly for biology/microscopy. Read and write TIFF stacks. Functions for segmentation, filtering and analyzing 3D point patterns.

Maintained by Volker Schmid. Last updated 3 years ago.

biology microscopy

18.8 match 4 stars 5.30 score 33 scripts 1 dependents

taylor-arnold

ggimg:Graphics Layers for Plotting Image Data with 'ggplot2'

Provides two new layer types for displaying image data as layers within the Grammar of Graphics framework. Displays images using either a rectangle interface, with a fixed bounding box, or a point interface using a central point and general size parameter. Images can be given as local JPEG or PNG files, external resources, or as a list column containing raster image data.

Maintained by Taylor B. Arnold. Last updated 1 years ago.

ggplot2-geom image-analysis

17.4 match 53 stars 5.70 score 19 scripts

yihui

xfun:Supporting Functions for Packages Maintained by 'Yihui Xie'

Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.

Maintained by Yihui Xie. Last updated 3 days ago.

5.5 match 145 stars 18.18 score 916 scripts 4.4k dependents

svkucheryavski

mdatools:Multivariate Data Analysis for Chemometrics

Projection based methods for preprocessing, exploring and analysis of multivariate data used in chemometrics. S. Kucheryavskiy (2020) <doi:10.1016/j.chemolab.2020.103937>.

Maintained by Sergey Kucheryavskiy. Last updated 8 months ago.

13.4 match 35 stars 7.37 score 220 scripts 1 dependents

csafe-isu

handwriter:Handwriting Analysis in R

Perform statistical writership analysis of scanned handwritten documents. Webpage provided at: <https://github.com/CSAFE-ISU/handwriter>.

Maintained by Stephanie Reinders. Last updated 1 months ago.

cpp jags

11.1 match 24 stars 8.70 score 27 scripts 2 dependents

ropensci

RSelenium:R Bindings for 'Selenium WebDriver'

Provides a set of R bindings for the 'Selenium 2.0 WebDriver' (see <https://www.selenium.dev/documentation/> for more information) using the 'JsonWireProtocol' (see <https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol> for more information). 'Selenium 2.0 WebDriver' allows driving a web browser natively as a user would either locally or on a remote machine using the Selenium server it marks a leap forward in terms of web browser automation. Selenium automates web browsers (commonly referred to as browsers). Using RSelenium you can automate browsers locally or remotely.

Maintained by Jonathan Völkle. Last updated 2 years ago.

rselenium selenium webdriver

7.2 match 344 stars 13.38 score 1.9k scripts 12 dependents

bioc

mixOmics:Omics Data Integration Project

Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.

Maintained by Eva Hamrud. Last updated 4 days ago.

immunooncology microarray sequencing metabolomics metagenomics proteomics geneprediction multiplecomparison classification regression bioconductor genomics genomics-data genomics-visualization multivariate-analysis multivariate-statistics omics r-pkg r-project

7.0 match 182 stars 13.71 score 1.3k scripts 22 dependents

gastonmaurodiaz

rcaiman:CAnopy IMage ANalysis

Tools for pre-processing and processing canopy photographs with support for raw data reading. Works with images taken with both regular and fisheye lenses (all types). Includes algorithms specifically designed to mitigate errors caused by direct sunlight.

Maintained by Gastón Mauro Díaz. Last updated 9 days ago.

27.1 match 1 stars 3.54 score 2 scripts

kumes

chatAI4R:Chat-Based Interactive Artificial Intelligence for R

The Large Language Model (LLM) represents a groundbreaking advancement in data science and programming, and also allows us to extend the world of R. A seamless interface for integrating the 'OpenAI' Web APIs into R is provided in this package. This package leverages LLM-based AI techniques, enabling efficient knowledge discovery and data analysis (see 'OpenAI' Web APIs details <https://openai.com/blog/openai-api>). The previous functions such as seamless translation and image generation have been moved to other packages 'deepRstudio' and 'stableDiffusion4R'.

Maintained by Satoshi Kume. Last updated 1 months ago.

ai bioinformatics chatgpt gpt image image-generation

21.6 match 14 stars 4.45 score 3 scripts

fcharte

mldr.datasets:R Ultimate Multilabel Dataset Repository

Large collection of multilabel datasets along with the functions needed to export them to several formats, to make partitions, and to obtain bibliographic information.

Maintained by David Charte. Last updated 6 years ago.

20.5 match 8 stars 4.68 score 120 scripts

s-u

png:Read and write PNG images

This package provides an easy and simple way to read, write and display bitmap images stored in the PNG format. It can read and write both files and in-memory raw vectors.

Maintained by Simon Urbanek. Last updated 2 years ago.

libpng

7.2 match 5 stars 13.07 score 7.5k scripts 2.2k dependents

bioc

xcms:LC-MS and GC-MS Data Analysis

Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.

Maintained by Steffen Neumann. Last updated 3 days ago.

immunooncology massspectrometry metabolomics bioconductor feature-detection mass-spectrometry peak-detection cpp

6.5 match 196 stars 14.31 score 984 scripts 11 dependents

r-spatial

leafem:'leaflet' Extensions for 'mapview'

Provides extensions for packages 'leaflet' & 'mapdeck', many of which are used by package 'mapview'. Focus is on functionality readily available in Geographic Information Systems such as 'Quantum GIS'. Includes functions to display coordinates of mouse pointer position, query image values via mouse pointer and zoom-to-layer buttons. Additionally, provides a feature type agnostic function to add points, lines, polygons to a map.

Maintained by Tim Appelhans. Last updated 18 days ago.

7.4 match 108 stars 12.36 score 704 scripts 53 dependents

bioc

beadarray:Quality assessment and low-level analysis for Illumina BeadArray data

The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

Maintained by Mark Dunning. Last updated 5 months ago.

microarray onechannel qualitycontrol preprocessing

11.6 match 7.88 score 70 scripts 4 dependents

bioc

marray:Exploratory analysis for two-color spotted microarray data

Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.

Maintained by Yee Hwa (Jean) Yang. Last updated 5 months ago.

microarray twochannel preprocessing

10.1 match 8.92 score 222 scripts 37 dependents

bioc

SpatialExperiment:S4 Class for Spatially Resolved -omics Data

Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform.

Maintained by Dario Righelli. Last updated 5 months ago.

datarepresentation dataimport infrastructure immunooncology geneexpression transcriptomics singlecell spatial

7.1 match 59 stars 12.63 score 1.8k scripts 71 dependents

rspatial

terra:Spatial Data Analysis

Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).

Maintained by Robert J. Hijmans. Last updated 1 days ago.

geospatial raster spatial vector onetbb proj gdal geos cpp

5.0 match 559 stars 17.64 score 17k scripts 851 dependents

fpaskali

LFApp:Shiny Apps for Lateral Flow Assays

Shiny apps for the quantitative analysis of images from lateral flow assays (LFAs). The images are segmented and background corrected and color intensities are extracted. The apps can be used to import and export intensity data and to calibrate LFAs by means of linear, loess, or gam models. The calibration models can further be saved and applied to intensity data from new images for determining concentrations.

Maintained by Filip Paskali. Last updated 10 months ago.

calibration image-processing medical-image-processing shiny

18.5 match 3 stars 4.78 score 2 scripts

adeverse

adegraphics:An S4 Lattice-Based Package for the Representation of Multivariate Data

Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.

Maintained by Aurélie Siberchicot. Last updated 8 months ago.

8.5 match 9 stars 10.37 score 386 scripts 6 dependents

dankelley

oce:Analysis of Oceanographic Data

Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature. This package is discussed extensively by Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.

Maintained by Dan Kelley. Last updated 2 days ago.

oceanography fortran cpp

5.7 match 146 stars 15.42 score 4.2k scripts 18 dependents

kjhealy

gssrdoc:Document General Social Survey Variable

The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.

Maintained by Kieran Healy. Last updated 11 months ago.

38.3 match 2.28 score 38 scripts

jonclayden

mmand:Mathematical Morphology in Any Number of Dimensions

Provides tools for performing mathematical morphology operations, such as erosion and dilation, on data of arbitrary dimensionality. Can also be used for finding connected components, resampling, filtering, smoothing and other image processing-style operations.

Maintained by Jon Clayden. Last updated 12 months ago.

image-processing morphology resampling cpp openmp

11.7 match 37 stars 7.42 score 223 scripts 9 dependents

zumbov2

colorizer:Colorize Old Images Using the 'DeOldify' Image Colorization API

Call the 'DeOldify' <https://github.com/jantic/DeOldify> image colorization API on 'DeepAI'<https://deepai.org/machine-learning-model/colorizer> to colorize black and white images.

Maintained by David Zumbach. Last updated 4 years ago.

colorization deoldify image

21.5 match 21 stars 4.02 score 3 scripts

stefanocoretta

rticulate:Articulatory Data Processing in R

A tool for processing Articulate Assistant Advanced™ (AAA) ultrasound tongue imaging data and Carstens AG500/1 electro-magnetic articulographic data.

Maintained by Stefano Coretta. Last updated 25 days ago.

phonetics software tongue-image ultrasound ultrasound-tongue-imaging

14.7 match 5 stars 5.88 score 17 scripts

modesto-escobar

netCoin:Interactive Analytic Networks

Create interactive analytic networks. It joins the data analysis power of R to obtain coincidences, co-occurrences and correlations, and the visualization libraries of 'JavaScript' in one package.

Maintained by Modesto Escobar. Last updated 16 days ago.

11.9 match 11 stars 7.22 score 47 scripts

bioc

imcRtools:Methods for imaging mass cytometry data analysis

This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected.

Maintained by Daniel Schulz. Last updated 5 months ago.

immunooncology singlecell spatial dataimport clustering imc single-cell

11.3 match 24 stars 7.58 score 126 scripts

s-u

jpeg:Read and write JPEG images

This package provides an easy and simple way to read, write and display bitmap images stored in the JPEG format. It can read and write both files and in-memory raw vectors.

Maintained by Simon Urbanek. Last updated 2 years ago.

libjpeg-turbo

7.2 match 7 stars 11.80 score 2.6k scripts 769 dependents

r-forge

Matrix:Sparse and Dense Matrix Classes and Methods

A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.

Maintained by Martin Maechler. Last updated 7 days ago.

openblas

4.9 match 1 stars 17.23 score 33k scripts 12k dependents

estfernan

SAFARI:Shape Analysis for AI-Reconstructed Images

Provides functionality for image processing and shape analysis in the context of reconstructed medical images generated by deep learning-based methods or standard image processing algorithms and produced from different medical imaging types, such as X-ray, Computational Tomography (CT), Magnetic Resonance Imaging (MRI), and pathology imaging. Specifically, offers tools to segment regions of interest and to extract quantitative shape descriptors for applications in signal processing, statistical analysis and modeling, and machine learning.

Maintained by Esteban Fernandez. Last updated 3 years ago.

reconstructed-images shape-analysis

21.5 match 2 stars 3.90 score 6 scripts

troyhill

coreCT:Programmatic Analysis of Sediment Cores Using Computed Tomography Imaging

Computed tomography (CT) imaging is a powerful tool for understanding the composition of sediment cores. This package streamlines and accelerates the analysis of CT data generated in the context of environmental science. Included are tools for processing raw DICOM images to characterize sediment composition (sand, peat, etc.). Root analyses are also enabled, including measures of external surface area and volumes for user-defined root size classes. For a detailed description of the application of computed tomography imaging for sediment characterization, see: Davey, E., C. Wigand, R. Johnson, K. Sundberg, J. Morris, and C. Roman. (2011) <DOI: 10.1890/10-2037.1>.

Maintained by Troy D. Hill. Last updated 4 years ago.

biomass computed-tomography sediment sediment-core

18.8 match 3 stars 4.41 score 17 scripts

ayrangi

WaveletComp:Computational Wavelet Analysis

Wavelet analysis and reconstruction of time series, cross-wavelets and phase-difference (with filtering options), significance with simulation algorithms.

Maintained by Angi Roesch. Last updated 7 years ago.

15.2 match 5 stars 5.39 score 181 scripts 5 dependents

r-hyperspec

hyperSpec:Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

Comfortable ways to work with hyperspectral data sets, i.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with each of the spectra. The spectra can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS, etc. More generally, any data that is recorded over a discretized variable, e.g. absorbance = f(wavelength), stored as a vector of absorbance values for discrete wavelengths is suitable.

Maintained by Claudia Beleites. Last updated 10 months ago.

data-wrangling hyperspectral imaging infrared nmr raman spectroscopy uv-vis xrf

10.0 match 16 stars 8.13 score 233 scripts 2 dependents

rogiersbart

ti:A single-channel UINT8 TIFF toolkit

The {ti} package provides a set of tools for working with single-channel unsigned 8-bit integer TIFF images.

Maintained by Bart Rogiers. Last updated 9 months ago.

32.9 match 2.46 score 58 scripts

cran

wavethresh:Wavelets Statistics and Transforms

Performs 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.

Maintained by Guy Nason. Last updated 7 months ago.

13.7 match 5.89 score 41 dependents

dkahle

ggmap:Spatial Visualization with ggplot2

A collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions for geolocation and routing.

Maintained by David Kahle. Last updated 1 years ago.

5.6 match 770 stars 14.17 score 12k scripts 31 dependents

fabnavarro

rwavelet:Wavelet Analysis

Perform wavelet analysis (orthogonal,translation invariant, tensorial, 1-2-3d transforms, thresholding, block thresholding, linear,...) with applications to data compression, denoising/regression or clustering. The core of the code is a port of 'MATLAB' Wavelab toolbox written by D. Donoho, A. Maleki and M. Shahram (<https://statweb.stanford.edu/~wavelab/>).

Maintained by Navarro Fabien. Last updated 7 months ago.

machine-learning regression wavelet

15.9 match 5 stars 5.01 score 41 scripts

joelcarlson

RImagePalette:Extract the Colors from Images

A pure R implementation of the median cut algorithm. Extracts the dominant colors from an image, and turns them into a scale for use in plots or for fun!

Maintained by Joel Carlson. Last updated 3 years ago.

16.4 match 46 stars 4.84 score 30 scripts

eogrady21

vprr:Processing and Visualization of Video Plankton Recorder Data

An oceanographic data processing package for analyzing and visualizing Video Plankton Recorder data. This package was developed at 'Bedford Institute of Oceanography'. Functions are designed to process automated image classification output and create organized and easily portable data products.

Maintained by Emily OGrady. Last updated 1 months ago.

14.0 match 2 stars 5.61 score 17 scripts

jonclayden

divest:Get Images Out of DICOM Format Quickly

Provides tools to sort DICOM-format medical image files, and convert them to NIfTI-1 format.

Maintained by Jon Clayden. Last updated 11 days ago.

conversion dicom medical-imaging openjpeg2 cpp

11.0 match 14 stars 7.09 score 30 scripts

emmanuelparadis

ape:Analyses of Phylogenetics and Evolution

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Maintained by Emmanuel Paradis. Last updated 16 hours ago.

openblas cpp

4.5 match 64 stars 17.22 score 13k scripts 599 dependents

davidgohel

flextable:Functions for Tabular Reporting

Use a grammar for creating and customizing pretty tables. The following formats are supported: 'HTML', 'PDF', 'RTF', 'Microsoft Word', 'Microsoft PowerPoint' and R 'Grid Graphics'. 'R Markdown', 'Quarto' and the package 'officer' can be used to produce the result files. The syntax is the same for the user regardless of the type of output to be produced. A set of functions allows the creation, definition of cell arrangement, addition of headers or footers, formatting and definition of cell content with text and or images. The package also offers a set of high-level functions that allow tabular reporting of statistical models and the creation of complex cross tabulations.

Maintained by David Gohel. Last updated 1 months ago.

docx html5 ms-office-documents rmarkdown table

4.5 match 583 stars 17.04 score 7.3k scripts 119 dependents

refunders

refund:Regression with Functional Data

Methods for regression for functional data, including function-on-scalar, scalar-on-function, and function-on-function regression. Some of the functions are applicable to image data.

Maintained by Julia Wrobel. Last updated 6 months ago.

7.5 match 41 stars 10.25 score 472 scripts 16 dependents

bioc

spatialHeatmap:spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

The spatialHeatmap package offers the primary functionality for visualizing cell-, tissue- and organ-specific assay data in spatial anatomical images. Additionally, it provides extended functionalities for large-scale data mining routines and co-visualizing bulk and single-cell data. A description of the project is available here: https://spatialheatmap.org.

Maintained by Jianhai Zhang. Last updated 4 months ago.

spatial visualization microarray sequencing geneexpression datarepresentation network clustering graphandnetwork cellbasedassays atacseq dnaseq tissuemicroarray singlecell cellbiology genetarget

11.9 match 5 stars 6.26 score 12 scripts

s-u

tiff:Read and Write TIFF Images

Functions to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors, including native image representation.

Maintained by Simon Urbanek. Last updated 1 years ago.

tiff

7.5 match 11 stars 10.02 score 616 scripts 129 dependents

tsuda16k

sketcher:Pencil Sketch Effect

An implementation of image processing effects that convert a photo into a line drawing image. For details, please refer to Tsuda, H. (2020). sketcher: An R package for converting a photo into a sketch style image. <doi:10.31234/osf.io/svmw5>.

Maintained by Hiroyuki Tsuda. Last updated 4 years ago.

15.2 match 48 stars 4.86 score 7 scripts

davidgohel

officer:Manipulation of Microsoft Word and PowerPoint Documents

Access and manipulate 'Microsoft Word', 'RTF' and 'Microsoft PowerPoint' documents from R. The package focuses on tabular and graphical reporting from R; it also provides two functions that let users get document content into data objects. A set of functions lets add and remove images, tables and paragraphs of text in new or existing documents. The package does not require any installation of Microsoft products to be able to write Microsoft files.

Maintained by David Gohel. Last updated 1 months ago.

ms-office-documents powerpoint word

4.6 match 630 stars 15.79 score 4.1k scripts 137 dependents

zivankaraman

CDSE:'Copernicus Data Space Ecosystem' API Wrapper

Provides interface to the 'Copernicus Data Space Ecosystem' API <https://dataspace.copernicus.eu/analyse/apis>, mainly for searching the catalog of available data from Copernicus Sentinel missions and obtaining the images for just the area of interest based on selected spectral bands. The package uses the 'Sentinel Hub' REST API interface <https://dataspace.copernicus.eu/analyse/apis/sentinel-hub> that provides access to various satellite imagery archives. It allows you to access raw satellite data, rendered images, statistical analysis, and other features. This package is in no way officially related to or endorsed by Copernicus.

Maintained by Zivan Karaman. Last updated 1 months ago.

copernicus earth-observation remote-sensing

14.9 match 15 stars 4.91 score 12 scripts

jonclayden

loder:Dependency-Free Access to PNG Image Files

Read and write access to PNG image files using the LodePNG library. The package has no external dependencies.

Maintained by Jon Clayden. Last updated 2 years ago.

image image-processing png

21.0 match 4 stars 3.48 score 15 scripts

carlos-alberto-silva

ICESat2VegR:NASA's Ice, Cloud, and Elevation Satellite (ICESat-2) Data Analysis for Land and Vegetation Applications

Set of tools for downloading, reading, visualizing, processing and exporting NASA's ICESat-2 ATL03 (Global Geolocated Photon Data) and ATL08 (Land and Vegetation Height) products for Land and Vegetation Applications.

Maintained by Caio Hamamura. Last updated 6 months ago.

gdal proj cpp

15.9 match 11 stars 4.57 score 21 scripts

tidymodels

probably:Tools for Post-Processing Predicted Values

Models can be improved by post-processing class probabilities, by: recalibration, conversion to hard probabilities, assessment of equivocal zones, and other activities. 'probably' contains tools for conducting these operations as well as calibration tools and conformal inference techniques for regression models.

Maintained by Max Kuhn. Last updated 5 months ago.

6.0 match 115 stars 12.09 score 21k scripts 1 dependents

cwatson

brainGraph:Graph Theory Analysis of Brain MRI Data

A set of tools for performing graph theory analysis of brain MRI data. It works with data from a Freesurfer analysis (cortical thickness, volumes, local gyrification index, surface area), diffusion tensor tractography data (e.g., from FSL) and resting-state fMRI data (e.g., from DPABI). It contains a graphical user interface for graph visualization and data exploration, along with several functions for generating useful figures.

Maintained by Christopher G. Watson. Last updated 1 years ago.

brain-connectivity brain-imaging complex-networks connectome connectomics fmri graph-theory mri network-analysis neuroimaging neuroscience statistics tractography

9.2 match 188 stars 7.86 score 107 scripts 3 dependents

rstudio

blastula:Easily Send HTML Email Messages

Compose and send out responsive HTML email messages that render perfectly across a range of email clients and device sizes. Helper functions let the user insert embedded images, web link buttons, and 'ggplot2' plot objects into the message body. Messages can be sent through an 'SMTP' server, through the 'Posit Connect' service, or through the 'Mailgun' API service <https://www.mailgun.com/>.

Maintained by Richard Iannone. Last updated 8 months ago.

easy-to-use email html markdown responsive-email smtp

7.0 match 552 stars 10.27 score 348 scripts 5 dependents

bioc

flowcatchR:Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells

flowcatchR is a set of tools to analyze in vivo microscopy imaging data, focused on tracking flowing blood cells. It guides the steps from segmentation to calculation of features, filtering out particles not of interest, providing also a set of utilities to help checking the quality of the performed operations (e.g. how good the segmentation was). It allows investigating the issue of tracking flowing cells such as in blood vessels, to categorize the particles in flowing, rolling and adherent. This classification is applied in the study of phenomena such as hemostasis and study of thrombosis development. Moreover, flowcatchR presents an integrated workflow solution, based on the integration with a Shiny App and Jupyter notebooks, which is delivered alongside the package, and can enable fully reproducible bioimage analysis in the R environment.

Maintained by Federico Marini. Last updated 3 months ago.

software visualization cellbiology classification infrastructure gui shinyapps bioconductor fluorescence microscopy particles tracking

12.7 match 4 stars 5.62 score 8 scripts

bioc

BiocGenerics:S4 generic functions used in Bioconductor

The package defines many S4 generic functions used in Bioconductor.

Maintained by Hervé Pagès. Last updated 1 months ago.

infrastructure bioconductor-package core-package

5.0 match 12 stars 14.22 score 612 scripts 2.2k dependents

r-spatial

leafpop:Include Tables, Images and Graphs in Leaflet Pop-Ups

Creates 'HTML' strings to embed tables, images or graphs in pop-ups of interactive maps created with packages like 'leaflet' or 'mapview'. Handles local images located on the file system or via remote URL. Handles graphs created with 'lattice' or 'ggplot2' as well as interactive plots created with 'htmlwidgets'.

Maintained by Tim Appelhans. Last updated 6 months ago.

7.2 match 114 stars 9.76 score 458 scripts 26 dependents

jefferis

readbitmap:Simple Unified Interface to Read Bitmap Images (BMP,JPEG,PNG,TIFF)

Identifies and reads Windows BMP, JPEG, PNG, and TIFF format bitmap images. Identification defaults to the use of the magic number embedded in the file rather than the file extension. Reading of JPEG and PNG image depends on libjpg and libpng libraries. See file INSTALL for details if necessary.

Maintained by Gregory Jefferis. Last updated 7 years ago.

bmp jpeg png tiff

8.7 match 4 stars 8.01 score 75 scripts 58 dependents

glotaran

TIMP:Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

A problem solving environment (PSE) for fitting separable nonlinear models to measurements arising in physics and chemistry experiments, as described by Mullen & van Stokkum (2007) <doi:10.18637/jss.v018.i03> for its use in fitting time resolved spectroscopy data, and as described by Laptenok et al. (2007) <doi:10.18637/jss.v018.i08> for its use in fitting Fluorescence Lifetime Imaging Microscopy (FLIM) data, in the study of Förster Resonance Energy Transfer (FRET). `TIMP` also serves as the computation backend for the `GloTarAn` software, a graphical user interface for the package, as described in Snellenburg et al. (2012) <doi:10.18637/jss.v049.i03>.

Maintained by Joris Snellenburg. Last updated 2 years ago.

parameter-estimation

14.4 match 3 stars 4.80 score 14 scripts 1 dependents

henrikbengtsson

aroma.core:Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.

Maintained by Henrik Bengtsson. Last updated 2 years ago.

microarray onechannel twochannel multichannel dataimport datarepresentation gui visualization preprocessing qualitycontrol acgh copynumbervariants

15.8 match 1 stars 4.30 score 16 scripts 6 dependents

bioc

InteractiveComplexHeatmap:Make Interactive Complex Heatmaps

This package can easily make heatmaps which are produced by the ComplexHeatmap package into interactive applications. It provides two types of interactivities: 1. on the interactive graphics device, and 2. on a Shiny app. It also provides functions for integrating the interactive heatmap widgets for more complex Shiny app development.

Maintained by Zuguang Gu. Last updated 5 months ago.

software visualization sequencing interactive-heatmaps

7.0 match 132 stars 9.69 score 128 scripts 4 dependents

gojiplus

clarifai:Access to Clarifai API

Get description of images from Clarifai API. For more information, see <http://clarifai.com>. Clarifai uses a large deep learning cloud to come up with descriptive labels of the things in an image. It also provides how confident it is about each of the labels.

Maintained by Gaurav Sood. Last updated 8 years ago.

clarifai clarifai-api

12.0 match 13 stars 5.49 score 24 scripts

kumes

GoogleImage2Array:Create Array Data from 2D Image Thumbnails via Google Image Search

Images are provided as an array dataset of 2D image thumbnails from Google Image Search <https://www.google.com/search>. This array data may be suitable for a training data of machine learning or deep learning as a first trial.

Maintained by Satoshi Kume. Last updated 2 years ago.

image

20.7 match 3 stars 3.18 score 1 scripts

coolbutuseless

picohdr:Read, Write and Manipulate High Dynamic Range Images

High Dynamic Range (HDR) images support a large range in luminosity between the lightest and darkest regions of an image. To capture this range, data in HDR images is often stored as floating point numbers and in formats that capture more data and channels than standard image types. This package supports reading and writing two types of HDR images; PFM (Portable Float Map) and OpenEXR images. HDR images can be converted to lower dynamic ranges (for viewing) using tone-mapping. A number of tone-mapping algorithms are included which are based on Reinhard (2002) "Photographic tone reproduction for digital images" <doi:10.1145/566654.566575>.

Maintained by Mike Cheng. Last updated 3 months ago.

15.3 match 4.30 score 5 scripts

cran

RIA:Radiomics Image Analysis Toolbox for Medial Images

Radiomics image analysis toolbox for 2D and 3D radiological images. RIA supports DICOM, NIfTI, nrrd and npy (numpy array) file formats. RIA calculates first-order, gray level co-occurrence matrix, gray level run length matrix and geometry-based statistics. Almost all calculations are done using vectorized formulas to optimize run speeds. Calculation of several thousands of parameters only takes minutes on a single core of a conventional PC. Detailed methodology has been published: Kolossvary et al. Circ: Cardiovascular Imaging. 2017;10(12):e006843 <doi: 10.1161/CIRCIMAGING.117.006843>.

Maintained by Marton Kolossvary. Last updated 1 years ago.

20.2 match 7 stars 3.24 score

reinhardfurrer

spam:SPArse Matrix

Set of functions for sparse matrix algebra. Differences with other sparse matrix packages are: (1) we only support (essentially) one sparse matrix format, (2) based on transparent and simple structure(s), (3) tailored for MCMC calculations within G(M)RF. (4) and it is fast and scalable (with the extension package spam64). Documentation about 'spam' is provided by vignettes included in this package, see also Furrer and Sain (2010) <doi:10.18637/jss.v036.i10>; see 'citation("spam")' for details.

Maintained by Reinhard Furrer. Last updated 2 months ago.

fortran openblas cpp

7.0 match 1 stars 9.26 score 420 scripts 433 dependents

kurthornik

mlbench:Machine Learning Benchmark Problems

A collection of artificial and real-world machine learning benchmark problems, including, e.g., several data sets from the UCI repository.

Maintained by Kurt Hornik. Last updated 3 months ago.

7.3 match 2 stars 8.93 score 5.0k scripts 55 dependents

yihui

animation:A Gallery of Animations in Statistics and Utilities to Create Animations

Provides functions for animations in statistics, covering topics in probability theory, mathematical statistics, multivariate statistics, non-parametric statistics, sampling survey, linear models, time series, computational statistics, data mining and machine learning. These functions may be helpful in teaching statistics and data analysis. Also provided in this package are a series of functions to save animations to various formats, e.g. Flash, 'GIF', HTML pages, 'PDF' and videos. 'PDF' animations can be inserted into 'Sweave' / 'knitr' easily.

Maintained by Yihui Xie. Last updated 2 years ago.

animation statistical-computing statistical-graphics statistics

5.3 match 208 stars 12.08 score 2.5k scripts 29 dependents

jdtuck

fdasrvf:Elastic Functional Data Analysis

Performs alignment, PCA, and modeling of multidimensional and unidimensional functions using the square-root velocity framework (Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014 <DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic analysis of functional data through phase and amplitude separation.

Maintained by J. Derek Tucker. Last updated 27 days ago.

openblas cpp openmp

8.2 match 11 stars 7.74 score 83 scripts 3 dependents

bioc

HPAanalyze:Retrieve and analyze data from the Human Protein Atlas

Provide functions for retrieving, exploratory analyzing and visualizing the Human Protein Atlas data.

Maintained by Anh Nhat Tran. Last updated 5 months ago.

proteomics cellbiology visualization software

8.5 match 35 stars 7.43 score 37 scripts

mlr-org

mlr3torch:Deep Learning with 'mlr3'

Deep Learning library that extends the mlr3 framework by building upon the 'torch' package. It allows to conveniently build, train, and evaluate deep learning models without having to worry about low level details. Custom architectures can be created using the graph language defined in 'mlr3pipelines'.

Maintained by Sebastian Fischer. Last updated 1 months ago.

data-science deep-learning machine-learning mlr3 torch

8.3 match 42 stars 7.63 score 78 scripts

rekyt

bnfimage:'BnF Image API' Client

Provides an R client for the image API of 'Bibliothèque Nationale de France' (BnF, National Library of France) <https://api.bnf.fr/api-iiif-de-recuperation-des-images-de-gallica#/>.

Maintained by Matthias Grenié. Last updated 4 years ago.

20.9 match 2 stars 3.00 score 5 scripts

ycphs

openxlsx:Read, Write and Edit xlsx Files

Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages with the added benefit of removing the dependency on Java.

Maintained by Jan Marvin Garbuszus. Last updated 2 months ago.

xlsx cpp

3.3 match 232 stars 18.98 score 20k scripts 270 dependents

julia-wrobel

mxfda:A Functional Data Analysis Package for Spatial Single Cell Data

Methods and tools for deriving spatial summary functions from single-cell imaging data and performing functional data analyses. Functions can be applied to other single-cell technologies such as spatial transcriptomics. Functional regression and functional principal component analysis methods are in the 'refund' package <https://cran.r-project.org/package=refund> while calculation of the spatial summary functions are from the 'spatstat' package <https://spatstat.org/>.

Maintained by Alex Soupir. Last updated 25 days ago.

11.8 match 1 stars 5.22 score 8 scripts

biagolini

bwimage:Describe Image Patterns in Natural Structures

A computational tool to describe patterns in black and white images from natural structures. 'bwimage' implemented functions for exceptionally broad subject. For instance, 'bwimage' provide examples that range from calculation of canopy openness, description of patterns in vertical vegetation structure, to patterns in bird nest structure.

Maintained by Carlos Biagolini-Jr.. Last updated 5 years ago.

16.6 match 3.70 score

coolbutuseless

tickle:Easily Build Tcl/Tk UIs

Wrap tcltk to make GUI creation easier.

Maintained by mikefc. Last updated 3 years ago.

10.4 match 125 stars 5.88 score 11 scripts

yonicd

slickR:Create Interactive Carousels with the 'JavaScript' 'Slick' Library

Create and customize interactive carousels using the 'Slick' 'JavaScript' library and the 'htmlwidgets' package. The carousels can contain plots produced in R, images, 'iframes', videos and other 'htmlwidgets'. These carousels can be created directly from the R console, and viewed in the 'RStudio' internal viewer, in 'Shiny' apps and R Markdown documents.

Maintained by Jonathan Sidi. Last updated 1 years ago.

htmlwidgets javascript slick

6.5 match 160 stars 9.37 score 199 scripts 1 dependents

adeverse

ade4:Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.

Maintained by Aurélie Siberchicot. Last updated 13 days ago.

openblas cpp

4.0 match 39 stars 14.96 score 2.2k scripts 256 dependents

kkholst

lava:Latent Variable Models

A general implementation of Structural Equation Models with latent variables (MLE, 2SLS, and composite likelihood estimators) with both continuous, censored, and ordinal outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>). Mixture latent variable models and non-linear latent variable models (Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>). The package also provides methods for graph exploration (d-separation, back-door criterion), simulation of general non-linear latent variable models, and estimation of influence functions for a broad range of statistical models.

Maintained by Klaus K. Holst. Last updated 2 months ago.

latent-variable-models simulation statistics structural-equation-models

4.7 match 33 stars 12.85 score 610 scripts 476 dependents

zumbov2

colorfindr:Extract Colors from Windows BMP, JPEG, PNG, TIFF, and SVG Format Images

Extracts colors from various image types, returns customized reports and plots treemaps and 3D scatterplots of image compositions. Color palettes can also be created.

Maintained by David Zumbach. Last updated 4 years ago.

3d-scatter-plot colors plotly treemap

11.0 match 141 stars 5.51 score 41 scripts

r-forge

colorspace:A Toolbox for Manipulating and Assessing Colors and Palettes

Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny graphical user interface) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Details can be found on the project web page at <https://colorspace.R-Forge.R-project.org/> and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical Software, <doi:10.18637/jss.v096.i01>).

Maintained by Achim Zeileis. Last updated 4 months ago.

3.7 match 16.23 score 8.2k scripts 8.1k dependents

mjlajeunesse

juicr:Automated and Manual Extraction of Numerical Data from Scientific Images

Provides a GUI interface for automating data extraction from multiple images containing scatter and bar plots, semi-automated tools to tinker with extraction attempts, and a fully-loaded point-and-click manual extractor with image zoom, calibrator, and classifier. Also provides detailed and R-independent extraction reports as fully-embedded .html records.

Maintained by Marc J. Lajeunesse. Last updated 4 years ago.

10.6 match 64 stars 5.65 score 14 scripts

bioimaginggroup

nucim:Nucleome Imaging Toolbox

Tools for 4D nucleome imaging. Quantitative analysis of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy. See Volker J. Schmid, Marion Cremer, Thomas Cremer (2017) <doi:10.1016/j.ymeth.2017.03.013>.

Maintained by Volker Schmid. Last updated 3 years ago.

13.3 match 2 stars 4.48 score 7 scripts

appsilon

shiny.fluent:Microsoft Fluent UI for Shiny Apps

A rich set of UI components for building Shiny applications, including inputs, containers, overlays, menus, and various utilities. All components from Fluent UI (the underlying JavaScript library) are available and have usage examples in R.

Maintained by Jakub Sobolewski. Last updated 10 months ago.

microsoft-fluent-ui react rhinoverse shiny

6.0 match 280 stars 9.91 score 656 scripts

bioc

heatmaps:Flexible Heatmaps for Functional Genomics and Sequence Features

This package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features.

Maintained by Malcolm Perry. Last updated 5 months ago.

visualization sequencematching functionalgenomics

11.3 match 5.23 score 19 scripts 1 dependents

natverse

nat.templatebrains:NeuroAnatomy Toolbox ('nat') Extension for Handling Template Brains

Extends package 'nat' (NeuroAnatomy Toolbox) by providing objects and functions for handling template brains.

Maintained by Gregory Jefferis. Last updated 2 years ago.

bridging-registrations image-registration natverse neuroanatomy neuroanatomy-toolbox

14.6 match 3 stars 4.05 score 37 scripts

pepijn-devries

AmigaFFH:Commodore Amiga File Format Handler

Modern software often poorly support older file formats. This package intends to handle many file formats that were native to the antiquated Commodore Amiga machine. This package focuses on file types from the older Amiga operating systems (<= 3.0). It will read and write specific file formats and coerces them into more contemporary data.

Maintained by Pepijn de Vries. Last updated 2 months ago.

13.9 match 4 stars 4.21 score 41 scripts

oobianom

r2resize:In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents

Automatic resizing toolbar for containers, images and tables. Various resizer or expandable container functionalities are also included. Most suitable to include in 'shiny', 'markdown' and 'quarto' documents.

Maintained by Obinna Obianom. Last updated 4 months ago.

card resize rmarkdown shiny

9.0 match 15 stars 6.44 score 23 scripts

edjnet

tidywikidatar:Explore 'Wikidata' Through Tidy Data Frames

Query 'Wikidata' API <https://www.wikidata.org/wiki/Wikidata:Main_Page> with ease, get tidy data frames in response, and cache data in a local database.

Maintained by Giorgio Comai. Last updated 8 months ago.

wikidata

7.3 match 26 stars 7.86 score 46 scripts 2 dependents

lisalibungan

shapeR:Collection and Analysis of Otolith Shape Data

Studies otolith shape variation among fish populations. Otoliths are calcified structures found in the inner ear of teleost fish and their shape has been known to vary among several fish populations and stocks, making them very useful in taxonomy, species identification and to study geographic variations. The package extends previously described software used for otolith shape analysis by allowing the user to automatically extract closed contour outlines from a large number of images, perform smoothing to eliminate pixel noise, choose from conducting either a Fourier or wavelet transform to the outlines and visualize the mean shape. The output of the package are independent Fourier or wavelet coefficients which can be directly imported into a wide range of statistical packages in R. The package might prove useful in studies of any two dimensional objects.

Maintained by Lisa Anne Libungan. Last updated 7 years ago.

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