Showing 200 of total 256 results (show query)
bioc
GSVA:Gene Set Variation Analysis for Microarray and RNA-Seq Data
Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.
Maintained by Robert Castelo. Last updated 9 days ago.
functionalgenomicsmicroarrayrnaseqpathwaysgenesetenrichmentgene-set-enrichmentgenomicspathway-enrichment-analysis
212 stars 14.74 score 1.6k scripts 19 dependents
dcomtois
summarytools:Tools to Quickly and Neatly Summarize Data
Data frame summaries, cross-tabulations, weight-enabled frequency tables and common descriptive (univariate) statistics in concise tables available in a variety of formats (plain ASCII, Markdown and HTML). A good point-of-entry for exploring data, both for experienced and new R users.
Maintained by Dominic Comtois. Last updated 4 days ago.
descriptive-statisticsfrequency-tablehtml-reportmarkdownpanderpandocpandoc-markdownrmarkdownrstudio
527 stars 14.62 score 2.9k scripts 6 dependentsbioc
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.
datarepresentationdataimportinfrastructureimmunooncologygeneexpressiontranscriptomicssinglecellspatial
59 stars 12.63 score 1.8k scripts 71 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.
animationstatistical-computingstatistical-graphicsstatistics
208 stars 12.13 score 2.5k scripts 28 dependents
guangchuangyu
hexSticker:Create Hexagon Sticker in R
Helper functions for creating reproducible hexagon sticker purely in R.
Maintained by Guangchuang Yu. Last updated 2 months ago.
ggplot2hexagon-stickerlogostickersvisualization
773 stars 11.79 score 1.3k scripts 8 dependentsguangchuangyu
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.
172 stars 11.16 score 2.4k scripts 20 dependents
egeulgen
pathfindR:Enrichment Analysis Utilizing Active Subnetworks
Enrichment analysis enables researchers to uncover mechanisms underlying a phenotype. However, conventional methods for enrichment analysis do not take into account protein-protein interaction information, resulting in incomplete conclusions. 'pathfindR' is a tool for enrichment analysis utilizing active subnetworks. The main function identifies active subnetworks in a protein-protein interaction network using a user-provided list of genes and associated p values. It then performs enrichment analyses on the identified subnetworks, identifying enriched terms (i.e. pathways or, more broadly, gene sets) that possibly underlie the phenotype of interest. 'pathfindR' also offers functionalities to cluster the enriched terms and identify representative terms in each cluster, to score the enriched terms per sample and to visualize analysis results. The enrichment, clustering and other methods implemented in 'pathfindR' are described in detail in Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR': An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Front. Genet. <doi:10.3389/fgene.2019.00858>.
Maintained by Ege Ulgen. Last updated 1 months ago.
active-subnetworksenrichmentpathwaypathway-enrichment-analysissubnetwork
187 stars 10.38 score 138 scriptsbioc
singleCellTK:Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. SCTK allows users to seamlessly integrate tools from various packages at different stages of the analysis workflow. A general "a la carte" workflow gives users the ability access to multiple methods for data importing, calculation of general QC metrics, doublet detection, ambient RNA estimation and removal, filtering, normalization, batch correction or integration, dimensionality reduction, 2-D embedding, clustering, marker detection, differential expression, cell type labeling, pathway analysis, and data exporting. Curated workflows can be used to run Seurat and Celda. Streamlined quality control can be performed on the command line using the SCTK-QC pipeline. Users can analyze their data using commands in the R console or by using an interactive Shiny Graphical User Interface (GUI). Specific analyses or entire workflows can be summarized and shared with comprehensive HTML reports generated by Rmarkdown. Additional documentation and vignettes can be found at camplab.net/sctk.
Maintained by Joshua David Campbell. Last updated 1 months ago.
singlecellgeneexpressiondifferentialexpressionalignmentclusteringimmunooncologybatcheffectnormalizationqualitycontroldataimportgui
182 stars 10.17 score 252 scripts
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 2 months ago.
72 stars 9.72 score 151 scripts 1 dependentsbioc
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.
immunooncologysoftwaresinglecellonechanneltwochannelmultiplecomparisonnormalizationdataimportbioimagingimaging-mass-cytometrysingle-cellspatial-analysis
32 stars 9.61 score 354 scripts 5 dependentsbioc
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 2 months ago.
datarepresentationtranscriptomicsspatial
49 stars 9.40 score 322 scripts 1 dependents
thebioengineer
camcorder:Record Your Plot History
Record and generate a 'gif' of your 'R' sessions plots. When creating a visualization, there is inevitably iteration and refinement that occurs. Automatically save the plots made to a specified directory, previewing them as they would be saved. Then combine all plots generated into a 'gif' to show the plot refinement over time.
Maintained by Ellis Hughes. Last updated 1 years ago.
210 stars 9.22 score 980 scripts
thomasp85
ggfx:Pixel Filters for 'ggplot2' and 'grid'
Provides a range of filters that can be applied to layers from the 'ggplot2' package and its extensions, along with other graphic elements such as guides and theme elements. The filters are applied at render time and thus uses the exact pixel dimensions needed.
Maintained by Thomas Lin Pedersen. Last updated 3 years ago.
170 stars 9.10 score 452 scripts 3 dependentsbioc
Banksy:Spatial transcriptomic clustering
Banksy is an R package that incorporates spatial information to cluster cells in a feature space (e.g. gene expression). To incorporate spatial information, BANKSY computes the mean neighborhood expression and azimuthal Gabor filters that capture gene expression gradients. These features are combined with the cell's own expression to embed cells in a neighbor-augmented product space which can then be clustered, allowing for accurate and spatially-aware cell typing and tissue domain segmentation.
Maintained by Joseph Lee. Last updated 26 days ago.
clusteringspatialsinglecellgeneexpressiondimensionreductionclustering-algorithmsingle-cell-omicsspatial-omics
90 stars 9.03 score 248 scriptsbioc
Voyager:From geospatial to spatial omics
SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data. The voyager package implements basic exploratory spatial data analysis (ESDA) methods for SFE. Univariate methods include univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and correlograms. Bivariate methods include Lee's L and cross variogram. Multivariate methods include MULTISPATI PCA and multivariate local Geary's C recently developed by Anselin. The Voyager package also implements plotting functions to plot SFE data and ESDA results.
Maintained by Lambda Moses. Last updated 3 months ago.
geneexpressionspatialtranscriptomicsvisualizationbioconductoredaesdaexploratory-data-analysisomicsspatial-statisticsspatial-transcriptomics
88 stars 8.71 score 173 scripts
statnet
statnet:Software Tools for the Statistical Analysis of Network Data
This package is designed to make it easy to install and load key packages from the 'statnet' suite in a single step. The `statnet` suite is a collection of packages for statistical network analysis that are designed to work together; they share common data representations, 'API' design and a uniform user interface. Together they provide an integrated set of tools for the exploration, visualization, statistical analysis, and simulation of many different forms of network data. Learn more about 'statnet' at <https://www.statnet.org>. Tutorials for many packages can be found at <https://github.com/statnet/Workshops/wiki>. For an introduction to functions in this package, type help(package='statnet').
Maintained by Martina Morris. Last updated 4 years ago.
41 stars 8.69 score 896 scriptsbioc
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 14 days ago.
biomedicalinformaticscellbiologyspatialclusteringdataimportimmunooncologyqualitycontrolsinglecellsoftwarevisualization
22 stars 8.59 score 69 scripts
ropensci
weatherOz:An API Client for Australian Weather and Climate Data Resources
Provides automated downloading, parsing and formatting of weather data for Australia through API endpoints provided by the Department of Primary Industries and Regional Development ('DPIRD') of Western Australia and by the Science and Technology Division of the Queensland Government's Department of Environment and Science ('DES'). As well as the Bureau of Meteorology ('BOM') of the Australian government precis and coastal forecasts, and downloading and importing radar and satellite imagery files. 'DPIRD' weather data are accessed through public 'APIs' provided by 'DPIRD', <https://www.agric.wa.gov.au/weather-api-20>, providing access to weather station data from the 'DPIRD' weather station network. Australia-wide weather data are based on data from the Australian Bureau of Meteorology ('BOM') data and accessed through 'SILO' (Scientific Information for Land Owners) Jeffrey et al. (2001) <doi:10.1016/S1364-8152(01)00008-1>. 'DPIRD' data are made available under a Creative Commons Attribution 3.0 Licence (CC BY 3.0 AU) license <https://creativecommons.org/licenses/by/3.0/au/deed.en>. SILO data are released under a Creative Commons Attribution 4.0 International licence (CC BY 4.0) <https://creativecommons.org/licenses/by/4.0/>. 'BOM' data are (c) Australian Government Bureau of Meteorology and released under a Creative Commons (CC) Attribution 3.0 licence or Public Access Licence ('PAL') as appropriate, see <http://www.bom.gov.au/other/copyright.shtml> for further details.
Maintained by Rodrigo Pires. Last updated 1 months ago.
dpirdbommeteorological-dataweather-forecastaustraliaweatherweather-datameteorologywestern-australiaaustralia-bureau-of-meteorologywestern-australia-agricultureaustralia-agricultureaustralia-climateaustralia-weatherapi-clientclimatedatarainfallweather-api
31 stars 8.47 score 40 scriptsstatnet
ndtv:Network Dynamic Temporal Visualizations
Renders dynamic network data from 'networkDynamic' objects as movies, interactive animations, or other representations of changing relational structures and attributes.
Maintained by Skye Bender-deMoll. Last updated 9 months ago.
52 stars 8.36 score 254 scripts 1 dependentsbioc
ggkegg:Analyzing and visualizing KEGG information using the grammar of graphics
This package aims to import, parse, and analyze KEGG data such as KEGG PATHWAY and KEGG MODULE. The package supports visualizing KEGG information using ggplot2 and ggraph through using the grammar of graphics. The package enables the direct visualization of the results from various omics analysis packages.
Maintained by Noriaki Sato. Last updated 2 months ago.
pathwaysdataimportkeggggplot2ggraphpathwaytidygraphvisualization
225 stars 8.08 score 30 scripts 1 dependentsbioc
spicyR:Spatial analysis of in situ cytometry data
The spicyR package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell-resolution spatial omics technologies. spicyR consists of three primary steps: (i) summarizing the degree of spatial localization between pairs of cell types for each image; (ii) modelling the variability in localization summary statistics as a function of cell counts and (iii) testing for changes in spatial localizations associated with a response variable.
Maintained by Ellis Patrick. Last updated 26 days ago.
singlecellcellbasedassaysspatial
9 stars 8.02 score 57 scripts 1 dependentsbioc
FLAMES:FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data
Semi-supervised isoform detection and annotation from both bulk and single-cell long read RNA-seq data. Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution.
Maintained by Changqing Wang. Last updated 19 days ago.
rnaseqsinglecelltranscriptomicsdataimportdifferentialsplicingalternativesplicinggeneexpressionlongreadzlibcurlbzip2xz-utilscpp
31 stars 7.95 score 12 scripts
yonicd
texPreview:Compile and Preview Snippets of 'LaTeX'
Compile snippets of 'LaTeX' directly into images from the R console to view in the 'RStudio' viewer pane, Shiny apps and 'RMarkdown' documents.
Maintained by Jonathan Sidi. Last updated 1 years ago.
52 stars 7.82 score 72 scripts
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 27 days ago.
39 stars 7.68 score 87 scripts
proteomicslab57357
UniprotR:Retrieving Information of Proteins from Uniprot
Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information, For detailed information kindly read the publication <https://www.sciencedirect.com/science/article/pii/S1874391919303859>.
Maintained by Mohamed Soudy. Last updated 3 years ago.
61 stars 7.65 score 89 scripts 1 dependents
walkerke
mapboxapi:R Interface to 'Mapbox' Web Services
Includes support for 'Mapbox' Navigation APIs, including directions, isochrones, and route optimization; the Search API for forward and reverse geocoding; the Maps API for interacting with 'Mapbox' vector tilesets and visualizing 'Mapbox' maps in R; and 'Mapbox Tiling Service' and 'tippecanoe' for generating map tiles. See <https://docs.mapbox.com/api/> for more information about the 'Mapbox' APIs.
Maintained by Kyle Walker. Last updated 2 months ago.
113 stars 7.62 score 304 scriptsbioc
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.
immunooncologysinglecellspatialdataimportclusteringimcsingle-cell
24 stars 7.58 score 126 scriptsbioc
nnSVG:Scalable identification of spatially variable genes in spatially-resolved transcriptomics data
Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more spatial locations.
Maintained by Lukas M. Weber. Last updated 1 months ago.
spatialsinglecelltranscriptomicsgeneexpressionpreprocessing
17 stars 7.57 score 183 scripts 1 dependentsropensci
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 12 months ago.
54 stars 7.45 score 52 scriptsropensci
terrainr:Landscape Visualizations in R and 'Unity'
Functions for the retrieval, manipulation, and visualization of 'geospatial' data, with an aim towards producing '3D' landscape visualizations in the 'Unity' '3D' rendering engine. Functions are also provided for retrieving elevation data and base map tiles from the 'USGS' National Map <https://apps.nationalmap.gov/services/>.
Maintained by Michael Mahoney. Last updated 9 months ago.
datasetsdemsmapmap-tilesmappingnational-mapnhdorthoimagerypeer-reviewedprogressrretrieve-dataterrainrunityunity-rendering-engineusgs
72 stars 7.40 score 87 scriptsbioc
standR:Spatial transcriptome analyses of Nanostring's DSP data in R
standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. standR allows data inspection, quality control, normalization, batch correction and evaluation with informative visualizations.
Maintained by Ning Liu. Last updated 2 months ago.
spatialtranscriptomicsgeneexpressiondifferentialexpressionqualitycontrolnormalizationexperimenthubsoftware
18 stars 7.39 score 45 scripts
16eagle
basemaps:Accessing Spatial Basemaps in R
A lightweight package to access spatial basemaps from open sources such as 'OpenStreetMap', 'Carto', 'Mapbox' and others in R.
Maintained by Jakob Schwalb-Willmann. Last updated 4 months ago.
basemapscartoesrimapboxmaptileropenstreetmaposmspatialstadiastamenthunderforest
60 stars 7.38 score 307 scripts
ryo-n7
tvthemes:TV Show Themes and Color Palettes for 'ggplot2' Graphics
Contains various 'ggplot2' themes and color palettes based on TV shows such as 'Game of Thrones', 'Brooklyn Nine-Nine', 'Avatar: The Last Airbender', 'Spongebob Squarepants', and more.
Maintained by Ryo Nakagawara. Last updated 1 years ago.
color-schemedata-vizggplot2ggplot2-themespalette-colorstv-seriestv-shows
140 stars 7.34 score 103 scripts
waldronlab
SingleCellMultiModal:Integrating Multi-modal Single Cell Experiment datasets
SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. We provide several multi-modal datasets including scNMT, 10X Multiome, seqFISH, CITEseq, SCoPE2, and others. The scope of the package is is to provide data for benchmarking and analysis. To cite, use the 'citation' function and see <https://doi.org/10.1371/journal.pcbi.1011324>.
Maintained by Marcel Ramos. Last updated 4 months ago.
experimentdatasinglecelldatareproducibleresearchexperimenthubgeobioconductor-packageu24ca289073
17 stars 7.29 score 60 scriptsbioc
TBSignatureProfiler:Profile RNA-Seq Data Using TB Pathway Signatures
Gene signatures of TB progression, TB disease, and other TB disease states have been validated and published previously. This package aggregates known signatures and provides computational tools to enlist their usage on other datasets. The TBSignatureProfiler makes it easy to profile RNA-Seq data using these signatures and includes common signature profiling tools including ASSIGN, GSVA, and ssGSEA. Original models for some gene signatures are also available. A shiny app provides some functionality alongside for detailed command line accessibility.
Maintained by Aubrey R. Odom. Last updated 3 months ago.
geneexpressiondifferentialexpressionbioconductor-packagebiomarkersgene-signaturestuberculosis
12 stars 7.25 score 23 scripts
nflverse
nflplotR:NFL Logo Plots in 'ggplot2' and 'gt'
A set of functions to visualize National Football League analysis in 'ggplot2' plots and 'gt' tables.
Maintained by Sebastian Carl. Last updated 5 days ago.
nflnflfastrnflstatsnflversesports-analyticssportsanalytics
19 stars 7.21 score 316 scripts 1 dependentsropensci
mapscanner:Print Maps, Draw on Them, Scan Them Back in
Enables preparation of maps to be printed and drawn on. Modified maps can then be scanned back in, and hand-drawn marks converted to spatial objects.
Maintained by Mark Padgham. Last updated 2 months ago.
90 stars 7.13 score 2 scripts
tychelab
CoSMoS:Complete Stochastic Modelling Solution
Makes univariate, multivariate, or random fields simulations precise and simple. Just select the desired time series or random fields’ properties and it will do the rest. CoSMoS is based on the framework described in Papalexiou (2018, <doi:10.1016/j.advwatres.2018.02.013>), extended for random fields in Papalexiou and Serinaldi (2020, <doi:10.1029/2019WR026331>), and further advanced in Papalexiou et al. (2021, <doi:10.1029/2020WR029466>) to allow fine-scale space-time simulation of storms (or even cyclone-mimicking fields).
Maintained by Kevin Shook. Last updated 4 years ago.
11 stars 7.10 score 77 scriptsguangchuangyu
meme:Create Meme
The word 'Meme' was originated from the book, 'The Selfish Gene', authored by Richard Dawkins (1976). It is a unit of culture that is passed from one generation to another and correlates to the gene, the unit of physical heredity. The internet memes are captioned photos that are intended to be funny, ridiculous. Memes behave like infectious viruses and travel from person to person quickly through social media. The 'meme' package allows users to make custom memes.
Maintained by Guangchuang Yu. Last updated 4 years ago.
45 stars 7.08 score 54 scripts
loelschlaeger
fHMM:Fitting Hidden Markov Models to Financial Data
Fitting (hierarchical) hidden Markov models to financial data via maximum likelihood estimation. See Oelschläger, L. and Adam, T. "Detecting Bearish and Bullish Markets in Financial Time Series Using Hierarchical Hidden Markov Models" (2021, Statistical Modelling) <doi:10.1177/1471082X211034048> for a reference on the method. A user guide is provided by the accompanying software paper "fHMM: Hidden Markov Models for Financial Time Series in R", Oelschläger, L., Adam, T., and Michels, R. (2024, Journal of Statistical Software) <doi:10.18637/jss.v109.i09>.
Maintained by Lennart Oelschläger. Last updated 7 days ago.
financehidden-markov-modelscppopenmp
17 stars 7.04 score 5 scriptsyonicd
carbonate:Interact with 'carbon.js'
Create beautiful images of source code using 'carbon.js'<https://carbon.now.sh/about>.
Maintained by Jonathan Sidi. Last updated 3 years ago.
212 stars 6.83 score 32 scripts
mrcaseb
ggpath:Robust Image Rendering Support for 'ggplot2'
A 'ggplot2' extension that enables robust image grobs in panels and theme elements.
Maintained by Sebastian Carl. Last updated 2 days ago.
37 stars 6.81 score 97 scripts 3 dependentsbioc
ggspavis:Visualization functions for spatial transcriptomics data
Visualization functions for spatial transcriptomics data. Includes functions to generate several types of plots, including spot plots, feature (molecule) plots, reduced dimension plots, spot-level quality control (QC) plots, and feature-level QC plots, for datasets from the 10x Genomics Visium and other technological platforms. Datasets are assumed to be in either SpatialExperiment or SingleCellExperiment format.
Maintained by Lukas M. Weber. Last updated 5 months ago.
spatialsinglecelltranscriptomicsgeneexpressionqualitycontroldimensionreduction
3 stars 6.80 score 264 scripts
yufree
pmd:Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis and Reactomics Analysis
Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062> and PMD based reactomics analysis proposed in Yu and Petrick (2020) <doi:10.1038/s42004-020-00403-z> for gas/liquid chromatography–mass spectrometry (GC/LC-MS) based non-targeted analysis. PMD analysis including GlobalStd algorithm and structure/reaction directed analysis. GlobalStd algorithm could found independent peaks in m/z-retention time profiles based on retention time hierarchical cluster analysis and frequency analysis of paired mass distances within retention time groups. Structure directed analysis could be used to find potential relationship among those independent peaks in different retention time groups based on frequency of paired mass distances. Reactomics analysis could also be performed to build PMD network, assign sources and make biomarker reaction discovery. GUIs for PMD analysis is also included as 'shiny' applications.
Maintained by Miao YU. Last updated 9 days ago.
mass-spectrometrymetabolomicsnon-target
10 stars 6.78 score 40 scripts
hegghammer
daiR:Interface with Google Cloud Document AI API
R interface for the Google Cloud Services 'Document AI API' <https://cloud.google.com/document-ai/> with additional tools for output file parsing and text reconstruction. 'Document AI' is a powerful server-based OCR service that extracts text and tables from images and PDF files with high accuracy. 'daiR' gives R users programmatic access to this service and additional tools to handle and visualize the output. See the package website <https://dair.info/> for more information and examples.
Maintained by Thomas Hegghammer. Last updated 5 months ago.
42 stars 6.77 score 40 scriptsbioc
escheR:Unified multi-dimensional visualizations with Gestalt principles
The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to spatially-resolved transcriptomics data, but also broadly to data visualized in 2D space, such as embedding visualizations. We provide this open source R package escheR, which is built off of the state-of-the-art ggplot2 visualization framework and can be seamlessly integrated into genomics toolboxes and workflows.
Maintained by Boyi Guo. Last updated 5 months ago.
spatialsinglecelltranscriptomicsvisualizationsoftwaremultidimensionalsingle-cellspatial-omics
6 stars 6.74 score 153 scripts 1 dependentsbioc
chimeraviz:Visualization tools for gene fusions
chimeraviz manages data from fusion gene finders and provides useful visualization tools.
Maintained by Stian Lågstad. Last updated 5 months ago.
37 stars 6.71 score 14 scriptsbioc
SpotSweeper:Spatially-aware quality control for spatial transcriptomics
Spatially-aware quality control (QC) software for both spot-level and artifact-level QC in spot-based spatial transcripomics, such as 10x Visium. These methods calculate local (nearest-neighbors) mean and variance of standard QC metrics (library size, unique genes, and mitochondrial percentage) to identify outliers spot and large technical artifacts.
Maintained by Michael Totty. Last updated 3 months ago.
softwarespatialtranscriptomicsqualitycontrolgeneexpressionbioconductorquality-controlspatial-transcriptomics
5 stars 6.66 score 77 scriptsyufree
enviGCMS:GC/LC-MS Data Analysis for Environmental Science
Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.
Maintained by Miao YU. Last updated 9 days ago.
environmentmass-spectrometrymetabolomics
17 stars 6.66 score 30 scripts 1 dependentsbioc
lisaClust:lisaClust: Clustering of Local Indicators of Spatial Association
lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data that has been segmented at a single-cell resolution.
Maintained by Ellis Patrick. Last updated 4 months ago.
singlecellcellbasedassaysspatial
3 stars 6.64 score 48 scripts
eagerai
kerastuneR:Interface to 'Keras Tuner'
'Keras Tuner' <https://keras-team.github.io/keras-tuner/> is a hypertuning framework made for humans. It aims at making the life of AI practitioners, hypertuner algorithm creators and model designers as simple as possible by providing them with a clean and easy to use API for hypertuning. 'Keras Tuner' makes moving from a base model to a hypertuned one quick and easy by only requiring you to change a few lines of code.
Maintained by Turgut Abdullayev. Last updated 12 months ago.
hyperparameter-tuninghypertuningkeraskeras-tunertensorflowtrial
34 stars 6.61 score 48 scripts
fbertran
Cascade:Selection, Reverse-Engineering and Prediction in Cascade Networks
A modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>.
Maintained by Frederic Bertrand. Last updated 2 years ago.
1 stars 6.56 score 40 scripts 2 dependentsbioc
SpotClean:SpotClean adjusts for spot swapping in spatial transcriptomics data
SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontaminate the spot swapping effect, thus increase the sensitivity and precision of downstream analyses.
Maintained by Zijian Ni. Last updated 5 months ago.
dataimportrnaseqsequencinggeneexpressionspatialsinglecelltranscriptomicspreprocessingrna-seqspatial-transcriptomics
31 stars 6.52 score 36 scriptsbioc
CatsCradle:This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters
This package addresses two broad areas. It allows for in-depth analysis of spatial transcriptomic data by identifying tissue neighbourhoods. These are contiguous regions of tissue surrounding individual cells. 'CatsCradle' allows for the categorisation of neighbourhoods by the cell types contained in them and the genes expressed in them. In particular, it produces Seurat objects whose individual elements are neighbourhoods rather than cells. In addition, it enables the categorisation and annotation of genes by producing Seurat objects whose elements are genes.
Maintained by Michael Shapiro. Last updated 13 days ago.
biologicalquestionstatisticalmethodgeneexpressionsinglecelltranscriptomicsspatial
3 stars 6.52 scorebioc
Statial:A package to identify changes in cell state relative to spatial associations
Statial is a suite of functions for identifying changes in cell state. The functionality provided by Statial provides robust quantification of cell type localisation which are invariant to changes in tissue structure. In addition to this Statial uncovers changes in marker expression associated with varying levels of localisation. These features can be used to explore how the structure and function of different cell types may be altered by the agents they are surrounded with.
Maintained by Farhan Ameen. Last updated 5 months ago.
singlecellspatialclassificationsingle-cell
5 stars 6.49 score 23 scripts
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.
3dbraindtifreesurfermeshmrineuroimagingresearchsurfacevisualizationvoxel
68 stars 6.49 score 15 scripts
daniel1noble
metaDigitise:Extract and Summarise Data from Published Figures
High-throughput, flexible and reproducible extraction of data from figures in primary research papers. metaDigitise() can extract data and / or automatically calculate summary statistics for users from box plots, bar plots (e.g., mean and errors), scatter plots and histograms.
Maintained by Daniel Noble. Last updated 10 months ago.
82 stars 6.46 score 35 scriptsbioc
MoleculeExperiment:Prioritising a molecule-level storage of Spatial Transcriptomics Data
MoleculeExperiment contains functions to create and work with objects from the new MoleculeExperiment class. We introduce this class for analysing molecule-based spatial transcriptomics data (e.g., Xenium by 10X, Cosmx SMI by Nanostring, and Merscope by Vizgen). This allows researchers to analyse spatial transcriptomics data at the molecule level, and to have standardised data formats accross vendors.
Maintained by Shila Ghazanfar. Last updated 5 months ago.
dataimportdatarepresentationinfrastructuresoftwarespatialtranscriptomics
12 stars 6.45 score 39 scripts
trelliscope
trelliscope:Create Interactive Multi-Panel Displays
Trelliscope enables interactive exploration of data frames of visualizations.
Maintained by Ryan Hafen. Last updated 7 months ago.
29 stars 6.43 score 117 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 5 months ago.
5 stars 6.36 score 23 scripts
r-lib
asciicast:Create 'Ascii' Screen Casts from R Scripts
Record 'asciicast' screen casts from R scripts. Convert them to animated SVG images, to be used in 'README' files, or blog posts. Includes 'asciinema-player' as an 'HTML' widget, and an 'asciicast' 'knitr' engine, to embed 'ascii' screen casts in 'Rmarkdown' documents.
Maintained by Gábor Csárdi. Last updated 6 months ago.
232 stars 6.34 score 8 scripts
sagirumati
DynareR:Bringing the Power of 'Dynare' to 'R', 'R Markdown', and 'Quarto'
It allows running 'Dynare' program from base R, R Markdown and Quarto. 'Dynare' is a software platform for handling a wide class of economic models, in particular dynamic stochastic general equilibrium ('DSGE') and overlapping generations ('OLG') models. This package does not only integrate R and Dynare but also serves as a 'Dynare' Knit-Engine for 'knitr' package. The package requires 'Dynare' (<https://www.dynare.org/>) and 'Octave' (<https://www.octave.org/download.html>). Write all your 'Dynare' commands in R or R Markdown chunk.
Maintained by Sagiru Mati. Last updated 5 months ago.
9 stars 6.29 score 143 scriptsbioc
signifinder:Collection and implementation of public transcriptional cancer signatures
signifinder is an R package for computing and exploring a compendium of tumor signatures. It allows to compute a variety of signatures, based on gene expression values, and return single-sample scores. Currently, signifinder contains more than 60 distinct signatures collected from the literature, relating to multiple tumors and multiple cancer processes.
Maintained by Stefania Pirrotta. Last updated 3 months ago.
geneexpressiongenetargetimmunooncologybiomedicalinformaticsrnaseqmicroarrayreportwritingvisualizationsinglecellspatialgenesignaling
7 stars 6.28 score 15 scripts
rickhelmus
patRoon:Workflows for Mass-Spectrometry Based Non-Target Analysis
Provides an easy-to-use interface to a mass spectrometry based non-target analysis workflow. Various (open-source) tools are combined which provide algorithms for extraction and grouping of features, extraction of MS and MS/MS data, automatic formula and compound annotation and grouping related features to components. In addition, various tools are provided for e.g. data preparation and cleanup, plotting results and automatic reporting.
Maintained by Rick Helmus. Last updated 9 days ago.
mass-spectrometrynon-targetcppopenjdk
65 stars 6.24 score 43 scriptsbioc
concordexR:Identify Spatial Homogeneous Regions with concordex
Spatial homogeneous regions (SHRs) in tissues are domains that are homogenous with respect to cell type composition. We present a method for identifying SHRs using spatial transcriptomics data, and demonstrate that it is efficient and effective at finding SHRs for a wide variety of tissue types. concordex relies on analysis of k-nearest-neighbor (kNN) graphs. The tool is also useful for analysis of non-spatial transcriptomics data, and can elucidate the extent of concordance between partitions of cells derived from clustering algorithms, and transcriptomic similarity as represented in kNN graphs.
Maintained by Kayla Jackson. Last updated 2 months ago.
singlecellclusteringspatialtranscriptomics
13 stars 6.23 score 13 scripts
dtharvey
eChem:Simulations for Electrochemistry Experiments
Simulates cyclic voltammetry, linear-sweep voltammetry (both with and without stirring of the solution), and single-pulse and double-pulse chronoamperometry and chronocoulometry experiments using the implicit finite difference method outlined in Gosser (1993, ISBN: 9781560810261) and in Brown (2015) <doi:10.1021/acs.jchemed.5b00225>. Additional functions provide ways to display and to examine the results of these simulations. The primary purpose of this package is to provide tools for use in courses in analytical chemistry.
Maintained by David Harvey. Last updated 6 years ago.
6 stars 6.11 score 27 scripts
revbayes
RevGadgets:Visualization and Post-Processing of 'RevBayes' Analyses
Processes and visualizes the output of complex phylogenetic analyses from the 'RevBayes' phylogenetic graphical modeling software.
Maintained by Carrie Tribble. Last updated 1 years ago.
13 stars 6.09 score 208 scriptsbioc
simpleSeg:A package to perform simple cell segmentation
Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained from multiple images.
Maintained by Ellis Patrick. Last updated 5 months ago.
classificationsurvivalsinglecellnormalizationspatialspatial-statistics
6.06 score 19 scripts 2 dependentsbioc
consensusOV:Gene expression-based subtype classification for high-grade serous ovarian cancer
This package implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer as described by Helland et al. (PLoS One, 2011), Bentink et al. (PLoS One, 2012), Verhaak et al. (J Clin Invest, 2013), and Konecny et al. (J Natl Cancer Inst, 2014). In addition, the package implements a consensus classifier, which consolidates and improves on the robustness of the proposed subtype classifiers, thereby providing reliable stratification of patients with HGS ovarian tumors of clearly defined subtype.
Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.
classificationclusteringdifferentialexpressiongeneexpressionmicroarraytranscriptomicscancer-datacancer-genomicscancer-researchexpression-databaseovarian-cancer
3 stars 5.98 score 15 scripts 1 dependents
camdenk
mlbplotR:Create 'ggplot2' and 'gt' Visuals with Major League Baseball Logos
Tools to help visualize Major League Baseball analysis in 'ggplot2' and 'gt'. You provide team/player information and 'mlbplotR' will transform that information into team colors, logos, or player headshots for graphics.
Maintained by Camden Kay. Last updated 5 months ago.
baseballggplot2sportsdataverse
21 stars 5.97 score 111 scripts
vincentarelbundock
tinysnapshot:Snapshots for Unit Tests using the 'tinytest' Framework
Snapshots for unit tests using the 'tinytest' framework for R. Includes expectations to test base R and 'ggplot2' plots as well as console output from print().
Maintained by Vincent Arel-Bundock. Last updated 14 days ago.
15 stars 5.95 score 4 scripts 1 dependentsbioc
DiscoRhythm:Interactive Workflow for Discovering Rhythmicity in Biological Data
Set of functions for estimation of cyclical characteristics, such as period, phase, amplitude, and statistical significance in large temporal datasets. Supporting functions are available for quality control, dimensionality reduction, spectral analysis, and analysis of experimental replicates. Contains a R Shiny web interface to execute all workflow steps.
Maintained by Matthew Carlucci. Last updated 5 months ago.
softwaretimecoursequalitycontrolvisualizationguiprincipalcomponentbioconductordata-visualizationoscillationsrhythm-detectionwebapp
13 stars 5.89 score 9 scriptsbioc
tidySpatialExperiment:SpatialExperiment with tidy principles
tidySpatialExperiment provides a bridge between the SpatialExperiment package and the tidyverse ecosystem. It creates an invisible layer that allows you to interact with a SpatialExperiment object as if it were a tibble; enabling the use of functions from dplyr, tidyr, ggplot2 and plotly. But, underneath, your data remains a SpatialExperiment object.
Maintained by William Hutchison. Last updated 5 months ago.
infrastructurernaseqgeneexpressionsequencingspatialtranscriptomicssinglecell
6 stars 5.88 score 12 scriptsbioc
SpaNorm:Spatially-aware normalisation for spatial transcriptomics data
This package implements the spatially aware library size normalisation algorithm, SpaNorm. SpaNorm normalises out library size effects while retaining biology through the modelling of smooth functions for each effect. Normalisation is performed in a gene- and cell-/spot- specific manner, yielding library size adjusted data.
Maintained by Dharmesh D. Bhuva. Last updated 5 months ago.
softwaregeneexpressiontranscriptomicsspatialcellbiology
9 stars 5.86 score 3 scriptsbioc
escape:Easy single cell analysis platform for enrichment
A bridging R package to facilitate gene set enrichment analysis (GSEA) in the context of single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize ssGSEA, GSVA, AUCell, and UCell-based enrichment calculations across individual cells.
Maintained by Nick Borcherding. Last updated 9 days ago.
softwaresinglecellclassificationannotationgenesetenrichmentsequencinggenesignalingpathways
5.84 score 138 scriptsbioc
SpatialExperimentIO:Read in Xenium, CosMx, MERSCOPE or STARmapPLUS data as SpatialExperiment object
Read in imaging-based spatial transcriptomics technology data. Current available modules are for Xenium by 10X Genomics, CosMx by Nanostring, MERSCOPE by Vizgen, or STARmapPLUS from Broad Institute. You can choose to read the data in as a SpatialExperiment or a SingleCellExperiment object.
Maintained by Yixing E. Dong. Last updated 2 months ago.
datarepresentationdataimportinfrastructuretranscriptomicssinglecellspatialgeneexpression
9 stars 5.81 score 16 scriptsbioc
EGSEA:Ensemble of Gene Set Enrichment Analyses
This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. EGSEA algorithm utilizes the analysis results of twelve prominent GSE algorithms in the literature to calculate collective significance scores for each gene set.
Maintained by Monther Alhamdoosh. Last updated 5 months ago.
immunooncologydifferentialexpressiongogeneexpressiongenesetenrichmentgeneticsmicroarraymultiplecomparisononechannelpathwaysrnaseqsequencingsoftwaresystemsbiologytwochannelmetabolomicsproteomicskegggraphandnetworkgenesignalinggenetargetnetworkenrichmentnetworkclassification
5.81 score 64 scriptsropensci
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.
26 stars 5.76 score 22 scripts
christopherkenny
bskyr:Interact with 'Bluesky' Social
Collect data from and make posts on 'Bluesky' Social via the Hypertext Transfer Protocol (HTTP) Application Programming Interface (API), as documented at <https://atproto.com/specs/xrpc>. This further supports broader queries to the Authenticated Transfer (AT) Protocol <https://atproto.com/> which 'Bluesky' Social relies on. Data is returned in a tidy format and posts can be made using a simple interface.
Maintained by Christopher T. Kenny. Last updated 9 days ago.
20 stars 5.70 score 23 scriptsbioc
scFeatures:scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction
scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types. These features can then be used for a variety of analyses using other software in Biocondutor.
Maintained by Yue Cao. Last updated 5 months ago.
cellbasedassayssinglecellspatialsoftwaretranscriptomics
11 stars 5.69 score 15 scriptsbioc
sosta:A package for the analysis of anatomical tissue structures in spatial omics data
sosta (Spatial Omics STructure Analysis) is a package for analyzing spatial omics data to explore tissue organization at the anatomical structure level. It reconstructs morphologically relevant structures based on molecular features or cell types. It further calculates a range of structural and shape metrics to quantitatively describe tissue architecture. The package is designed to integrate with other packages for the analysis of spatial (omics) data.
Maintained by Samuel Gunz. Last updated 9 days ago.
softwarespatialtranscriptomicsvisualization
1 stars 5.68 score 2 scripts 1 dependents
selcukorkmaz
PubChemR:Interface to the 'PubChem' Database for Chemical Data Retrieval
Provides an interface to the 'PubChem' database via the PUG REST <https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest> and PUG View <https://pubchem.ncbi.nlm.nih.gov/docs/pug-view> services. This package allows users to automatically access chemical and biological data from 'PubChem', including compounds, substances, assays, and various other data types. Functions are available to retrieve data in different formats, perform searches, and access detailed annotations.
Maintained by Selcuk Korkmaz. Last updated 6 months ago.
2 stars 5.62 score 23 scriptsfbertran
SelectBoost:A General Algorithm to Enhance the Performance of Variable Selection Methods in Correlated Datasets
An implementation of the selectboost algorithm (Bertrand et al. 2020, 'Bioinformatics', <doi:10.1093/bioinformatics/btaa855>), which is a general algorithm that improves the precision of any existing variable selection method. This algorithm is based on highly intensive simulations and takes into account the correlation structure of the data. It can either produce a confidence index for variable selection or it can be used in an experimental design planning perspective.
Maintained by Frederic Bertrand. Last updated 2 years ago.
confidencecorrelationcorrelation-structuremodellingprecisionrecallselection-algorithm
7 stars 5.61 score 13 scripts 1 dependents
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 2 months ago.
2 stars 5.61 score 17 scripts
rafael-ayala
openSkies:Retrieval, Analysis and Visualization of Air Traffic Data
Provides functionalities and data structures to retrieve, analyze and visualize aviation data. It includes a client interface to the 'OpenSky' API <https://opensky-network.org>. It allows retrieval of flight information, as well as aircraft state vectors.
Maintained by Rafael Ayala. Last updated 12 months ago.
11 stars 5.60 score 36 scripts
dnme-minturdep
comunicacion:DNMyE - Comunicación
Herramientas para la comunicación de la Dirección Nacional de Mercados y Estadística de la Subsecretaría de Turismo de Argentina.
Maintained by Juan Pablo Ruiz Nicolini. Last updated 8 months ago.
4 stars 5.57 score 124 scripts 1 dependents
ardata-fr
doconv:Document Conversion to 'PDF' or 'PNG'
It provides the ability to generate images from documents of different types. Three main features are provided: functions for generating document thumbnails, functions for performing visual tests of documents and a function for updating fields and table of contents of a 'Microsoft Word' or 'RTF' document. In order to work, 'LibreOffice' must be installed on the machine and or 'Microsoft Word'. If the latter is available, it can be used to produce PDF documents or images identical to the originals; otherwise, 'LibreOffice' is used and the rendering can be sometimes different from the original documents.
Maintained by David Gohel. Last updated 6 months ago.
16 stars 5.54 score 28 scripts 1 dependents
glottospace
glottospace:Language Mapping and Geospatial Analysis of Linguistic and Cultural Data
Streamlined workflows for geolinguistic analysis, including: accessing global linguistic and cultural databases, data import, data entry, data cleaning, data exploration, mapping, visualization and export.
Maintained by Rui Dong. Last updated 4 months ago.
23 stars 5.54 score 6 scripts
biometris
statgenHTP:High Throughput Phenotyping (HTP) Data Analysis
Phenotypic analysis of data coming from high throughput phenotyping (HTP) platforms, including different types of outlier detection, spatial analysis, and parameter estimation. The package is being developed within the EPPN2020 project (<https://eppn2020.plant-phenotyping.eu/>). Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r/>).
Maintained by Bart-Jan van Rossum. Last updated 3 months ago.
geneticshigh-troughput-phenotyping
5 stars 5.53 score 17 scriptsbioc
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.
immunooncologysoftwaresinglecellonechanneltwochannelmultichannelspatialdataimportbioconductorimagingshinyvisualization
7 stars 5.50 score 15 scriptsbioc
VisiumIO:Import Visium data from the 10X Space Ranger pipeline
The package allows users to readily import spatial data obtained from either the 10X website or from the Space Ranger pipeline. Supported formats include tar.gz, h5, and mtx files. Multiple files can be imported at once with *List type of functions. The package represents data mainly as SpatialExperiment objects.
Maintained by Marcel Ramos. Last updated 2 months ago.
softwareinfrastructuredataimportsinglecellspatialbioconductor-packagegenomicsu24ca289073
5.50 score 14 scripts 1 dependentsnflverse
nflverse:Easily Install and Load the 'nflverse'
The 'nflverse' is a set of packages dedicated to data of the National Football League. This package is designed to make it easy to install and load multiple 'nflverse' packages in a single step. Learn more about the 'nflverse' at <https://nflverse.nflverse.com/>.
Maintained by Sebastian Carl. Last updated 2 days ago.
29 stars 5.47 score 204 scriptsloelschlaeger
RprobitB:Bayesian Probit Choice Modeling
Bayes estimation of probit choice models, both in the cross-sectional and panel setting. The package can analyze binary, multivariate, ordered, and ranked choices, as well as heterogeneity of choice behavior among deciders. The main functionality includes model fitting via Markov chain Monte Carlo m ethods, tools for convergence diagnostic, choice data simulation, in-sample and out-of-sample choice prediction, and model selection using information criteria and Bayes factors. The latent class model extension facilitates preference-based decider classification, where the number of latent classes can be inferred via the Dirichlet process or a weight-based updating heuristic. This allows for flexible modeling of choice behavior without the need to impose structural constraints. For a reference on the method see Oelschlaeger and Bauer (2021) <https://trid.trb.org/view/1759753>.
Maintained by Lennart Oelschläger. Last updated 6 months ago.
bayesdiscrete-choiceprobitopenblascppopenmp
4 stars 5.45 score 1 scripts
tombeesley
eyetools:Analyse Eye Data
Enables the automation of actions across the pipeline, including initial steps of transforming binocular data and gap repair to event-based processing such as fixations, saccades, and entry/duration in Areas of Interest (AOIs). It also offers visualisation of eye movement and AOI entries. These tools take relatively raw (trial, time, x, and y form) data and can be used to return fixations, saccades, and AOI entries and time spent in AOIs. As the tools rely on this basic data format, the functions can work with data from any eye tracking device. Implements fixation and saccade detection using methods proposed by Salvucci and Goldberg (2000) <doi:10.1145/355017.355028>.
Maintained by Tom Beesley. Last updated 3 months ago.
areas-of-interestattention-visualizationcognitive-sciencedwell-time-algorithmeye-trackereye-trackingeyetrackingggplot2psychologypsychology-experimentssaccadestobiitobii-eye-trackervisualization
4 stars 5.45 score 8 scripts
wjschne
ggdiagram:Object-Oriented Diagram Plots with ggplot2
The ggdiagram package creates path diagrams with an object-oriented approach and plots diagrams with ggplot2.
Maintained by W. Joel Schneider. Last updated 7 days ago.
diagramsfactor-analysisggplot2path-analysiss7structural-equation-modeling
32 stars 5.43 score
lter
lterpalettefinder:Extract Color Palettes from Photos and Pick Official LTER Palettes
Allows identification of palettes derived from LTER (Long Term Ecological Research) photographs based on user criteria. Also facilitates extraction of palettes from users' photos directly.
Maintained by Nicholas J Lyon. Last updated 2 years ago.
color-palette-generatordata-science
27 stars 5.43 score 7 scriptsbioc
UMI4Cats:UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
UMI-4C is a technique that allows characterization of 3D chromatin interactions with a bait of interest, taking advantage of a sonication step to produce unique molecular identifiers (UMIs) that help remove duplication bias, thus allowing a better differential comparsion of chromatin interactions between conditions. This package allows processing of UMI-4C data, starting from FastQ files provided by the sequencing facility. It provides two statistical methods for detecting differential contacts and includes a visualization function to plot integrated information from a UMI-4C assay.
Maintained by Mireia Ramos-Rodriguez. Last updated 5 months ago.
qualitycontrolpreprocessingalignmentnormalizationvisualizationsequencingcoveragechromatinchromatin-interactiongenomicsumi4c
5 stars 5.40 score 7 scriptsloelschlaeger
oeli:Utilities for Developing Data Science Software
Some general helper functions that I (and maybe others) find useful when developing data science software.
Maintained by Lennart Oelschläger. Last updated 4 months ago.
2 stars 5.38 score 1 scripts 4 dependents
bradyajohnston
figpatch:Easily Arrange External Figures with Patchwork Alongside 'ggplot2' Figures
For including external figures into an assembled {patchwork}. This enables the creation of more complex figures that include images alongside plots.
Maintained by Brady Johnston. Last updated 2 months ago.
alignmentggplot2patchworkrmarkdown
77 stars 5.37 score 61 scripts
igordot
clustermole:Unbiased Single-Cell Transcriptomic Data Cell Type Identification
Assignment of cell type labels to single-cell RNA sequencing (scRNA-seq) clusters is often a time-consuming process that involves manual inspection of the cluster marker genes complemented with a detailed literature search. This is especially challenging when unexpected or poorly described populations are present. The clustermole R package provides methods to query thousands of human and mouse cell identity markers sourced from a variety of databases.
Maintained by Igor Dolgalev. Last updated 1 years ago.
cell-typecell-type-annotationcell-type-classificationcell-type-identificationcell-type-matchinggene-expression-signaturesscrna-seqsingle-cell
13 stars 5.37 score 36 scriptsbioc
visiumStitched:Enable downstream analysis of Visium capture areas stitched together with Fiji
This package provides helper functions for working with multiple Visium capture areas that overlap each other. This package was developed along with the companion example use case data available from https://github.com/LieberInstitute/visiumStitched_brain. visiumStitched prepares SpaceRanger (10x Genomics) output files so you can stitch the images from groups of capture areas together with Fiji. Then visiumStitched builds a SpatialExperiment object with the stitched data and makes an artificial hexogonal grid enabling the seamless use of spatial clustering methods that rely on such grid to identify neighboring spots, such as PRECAST and BayesSpace. The SpatialExperiment objects created by visiumStitched are compatible with spatialLIBD, which can be used to build interactive websites for stitched SpatialExperiment objects. visiumStitched also enables casting SpatialExperiment objects as Seurat objects.
Maintained by Nicholas J. Eagles. Last updated 4 months ago.
softwarespatialtranscriptomicstranscriptiongeneexpressionvisualizationdataimport10xgenomicsbioconductorspatial-transcriptomicsspatialexperimentspatiallibdvisium
1 stars 5.36 score 4 scripts
doehm
cropcircles:Crops an Image to a Circle
Images are cropped to a circle with a transparent background. The function takes a vector of images, either local or from a link, and circle crops the image. Paths to the cropped image are returned for plotting with 'ggplot2'. Also includes cropping to a hexagon, heart, parallelogram, and square.
Maintained by Daniel Oehm. Last updated 1 years ago.
40 stars 5.35 score 111 scriptsbioc
hoodscanR:Spatial cellular neighbourhood scanning in R
hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based cell clustering.
Maintained by Ning Liu. Last updated 2 months ago.
spatialtranscriptomicssinglecellclusteringcpp
4 stars 5.32 score 15 scripts
unhcr-dataviz
unhcrdown:UNHCR Branded Templates for R Markdown Documents
Create United Nations High Commissioner for Refugees (UNHCR) branded documents, presentations, and reports using R Markdown templates. This package provides customized formats that align with UNHCR's official brand guidelines for creating professional PDF reports, Word documents, PowerPoint presentations, and HTML outputs.
Maintained by Cédric Vidonne. Last updated 2 months ago.
pagedownrmarkdownrmarkdown-templatexaringan
21 stars 5.32 score 1 scripts
aftonsteps
ggalignment:Plots 'D&D'-Style Alignment Charts
'D&D' alignment charts show 9 boxes with values for good through evil and values for chaotic through lawful. This package easily creates these alignment charts from user-provided image paths and alignment values.
Maintained by Afton Coombs. Last updated 28 days ago.
10 stars 5.30 score 6 scriptsbioc
ReactomeGraph4R:Interface for the Reactome Graph Database
Pathways, reactions, and biological entities in Reactome knowledge are systematically represented as an ordered network. Instances are represented as nodes and relationships between instances as edges; they are all stored in the Reactome Graph Database. This package serves as an interface to query the interconnected data from a local Neo4j database, with the aim of minimizing the usage of Neo4j Cypher queries.
Maintained by Chi-Lam Poon. Last updated 5 months ago.
dataimportpathwaysreactomenetworkgraphandnetwork
6 stars 5.26 score 6 scripts
simondedman
movegroup:Visualizing and Quantifying Space Use Data for Groups of Animals
Offers an easy and automated way to scale up individual-level space use analysis to that of groups. Contains a function from the 'move' package to calculate a dynamic Brownian bridge movement model from movement data for individual animals, as well as functions to visualize and quantify space use for individuals aggregated in groups. Originally written with passive acoustic telemetry in mind, this package also provides functionality to account for unbalanced acoustic receiver array designs, and satellite tag data.
Maintained by Simon Dedman. Last updated 2 months ago.
brownian-bridgehome-rangehome-range-analysismigrationresidencyspace-usetracking
18 stars 5.26 score 4 scripts
bioc
BulkSignalR:Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics
Inference of ligand-receptor (LR) interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics. BulkSignalR bases its inferences on the LRdb database included in our other package, SingleCellSignalR available from Bioconductor. It relies on a statistical model that is specific to bulk data sets. Different visualization and data summary functions are proposed to help navigating prediction results.
Maintained by Jean-Philippe Villemin. Last updated 3 months ago.
networkrnaseqsoftwareproteomicstranscriptomicsnetworkinferencespatial
5.22 score 15 scripts
eddelbuettel
ttdo:Extend 'tinytest' with 'diffobj' and 'tinysnapshot'
The 'tinytest' package offers a light-weight zero-dependency unit-testing framework to which this package adds support via the 'diffobj' package for 'diff'-style textual comparison of R objects, as well as via 'tinysnapshot' package for visual differences in plots.
Maintained by Dirk Eddelbuettel. Last updated 2 months ago.
21 stars 5.20 score 2 scriptsbioc
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.
statisticalmethodspatialbiomedicalinformatics
2 stars 5.18 score 25 scriptsbioc
spatialFDA:A Tool for Spatial Multi-sample Comparisons
spatialFDA is a package to calculate spatial statistics metrics. The package takes a SpatialExperiment object and calculates spatial statistics metrics using the package spatstat. Then it compares the resulting functions across samples/conditions using functional additive models as implemented in the package refund. Furthermore, it provides exploratory visualisations using functional principal component analysis, as well implemented in refund.
Maintained by Martin Emons. Last updated 1 months ago.
softwarespatialtranscriptomics
3 stars 5.18 score 6 scripts
ropengov
rogtemplate:'pkgdown' Template for 'rOpenGov' Packages
This is a private template for use by core rOpenGov packages. Please don’t use for your own code.
Maintained by Diego Hernangómez. Last updated 12 days ago.
ropengovtemplategithub-actionspkgdownpkgdown-template
2 stars 5.16 score 3 scripts
bioc
smoppix:Analyze Single Molecule Spatial Omics Data Using the Probabilistic Index
Test for univariate and bivariate spatial patterns in spatial omics data with single-molecule resolution. The tests implemented allow for analysis of nested designs and are automatically calibrated to different biological specimens. Tests for aggregation, colocalization, gradients and vicinity to cell edge or centroid are provided.
Maintained by Stijn Hawinkel. Last updated 1 months ago.
transcriptomicsspatialsinglecellcpp
1 stars 5.10 score 4 scripts
jonocarroll
mathpix:Support for the 'Mathpix' API (Image to 'LaTeX')
Given an image of a formula (typeset or handwritten) this package provides calls to the 'Mathpix' service to produce the 'LaTeX' code which should generate that image, and pastes it into a (e.g. an 'rmarkdown') document. See <https://docs.mathpix.com/> for full details. 'Mathpix' is an external service and use of the API is subject to their terms and conditions.
Maintained by Jonathan Carroll. Last updated 11 months ago.
249 stars 5.10 score 6 scriptsbioc
scider:Spatial cell-type inter-correlation by density in R
scider is a user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for serveral downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.
Maintained by Yunshun Chen. Last updated 5 months ago.
3 stars 5.08 score 3 scriptsbioc
BioCartaImage:BioCarta Pathway Images
The core functionality of the package is to provide coordinates of genes on the BioCarta pathway images and to provide methods to add self-defined graphics to the genes of interest.
Maintained by Zuguang Gu. Last updated 5 months ago.
softwarepathwaysbiocartavisualization
11 stars 5.04 score 6 scriptsbioc
alabaster.spatial:Save and Load Spatial 'Omics Data to/from File
Save SpatialExperiment objects and their images into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.
Maintained by Aaron Lun. Last updated 5 months ago.
5.02 score 5 scripts 1 dependentsbioc
jazzPanda:Finding spatially relevant marker genes in image based spatial transcriptomics data
This package contains the function to find marker genes for image-based spatial transcriptomics data. There are functions to create spatial vectors from the cell and transcript coordiantes, which are passed as inputs to find marker genes. Marker genes are detected for every cluster by two approaches. The first approach is by permtuation testing, which is implmented in parallel for finding marker genes for one sample study. The other approach is to build a linear model for every gene. This approach can account for multiple samples and backgound noise.
Maintained by Melody Jin. Last updated 28 days ago.
spatialgeneexpressiondifferentialexpressionstatisticalmethodtranscriptomicscorrelationlinear-modelsmarker-genesspatial-transcriptomics
2 stars 5.00 score
hughjonesd
anim.plots:Simple Animated Plots for R
Simple animated versions of basic R plots, using the 'animation' package. Includes animated versions of plot, barplot, persp, contour, filled.contour, hist, curve, points, lines, text, symbols, segments, and arrows.
Maintained by David Hugh-Jones. Last updated 4 years ago.
8 stars 5.00 score 25 scripts
alphaprime7
normfluodbf:Cleans and Normalizes FLUOstar DBF and DAT Files from 'Liposome' Flux Assays
Cleans and Normalizes FLUOstar DBF and DAT Files obtained from liposome flux assays. Users should verify extended usage of the package on files from other assay types.
Maintained by Tingwei Adeck. Last updated 5 months ago.
1 stars 4.98 score 12 scripts
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-segmentationkerastensorflow
18 stars 4.95 score 9 scripts
azvoleff
gfcanalysis:Tools for Working with Hansen et al. Global Forest Change Dataset
Supports analyses using the Global Forest Change dataset released by Hansen et al. gfcanalysis was originally written for the Tropical Ecology Assessment and Monitoring (TEAM) Network. For additional details on the Global Forest Change dataset, see: Hansen, M. et al. 2013. "High-Resolution Global Maps of 21st-Century Forest Cover Change." Science 342 (15 November): 850-53. The forest change data and more information on the product is available at <http://earthenginepartners.appspot.com>.
Maintained by Matthew Cooper. Last updated 1 years ago.
17 stars 4.93 score 33 scripts
djnavarro
jasmines:Generative Art
It doesn't do much, really.
Maintained by Danielle Navarro. Last updated 4 years ago.
112 stars 4.90 score 141 scripts
andrewdhawan
sigQC:Quality Control Metrics for Gene Signatures
Provides gene signature quality control metrics in publication ready plots. Namely, enables the visualization of properties such as expression, variability, correlation, and comparison of methods of standardisation and scoring metrics.
Maintained by Andrew Dhawan. Last updated 7 months ago.
4 stars 4.89 score 13 scripts
diegommcc
SpatialDDLS:Deconvolution of Spatial Transcriptomics Data Based on Neural Networks
Deconvolution of spatial transcriptomics data based on neural networks and single-cell RNA-seq data. SpatialDDLS implements a workflow to create neural network models able to make accurate estimates of cell composition of spots from spatial transcriptomics data using deep learning and the meaningful information provided by single-cell RNA-seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> and Mañanes et al. (2024) <doi:10.1093/bioinformatics/btae072> to get an overview of the method and see some examples of its performance.
Maintained by Diego Mañanes. Last updated 5 months ago.
deconvolutiondeep-learningneural-networkspatial-transcriptomics
5 stars 4.88 score 1 scripts
flavjack
huito:Reproducible and Flexible Label Design
An open-source R package to deploys reproducible and flexible labels using layers. The 'huito' package is part of the 'inkaverse' project for developing different procedures and tools used in plant science and experimental designs. Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Maintained by Flavio Lozano-Isla. Last updated 7 months ago.
1 stars 4.79 score 31 scriptsloelschlaeger
ao:Alternating Optimization
Alternating optimization is an iterative procedure that optimizes a function by alternately performing restricted optimization over individual parameter subsets. Instead of tackling joint optimization directly, it breaks the problem down into simpler sub-problems. This approach can make optimization feasible when joint optimization is too difficult.
Maintained by Lennart Oelschläger. Last updated 8 months ago.
2 stars 4.78 score 2 scriptsbioc
spatialDE:R wrapper for SpatialDE
SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk.
Maintained by Gabriele Sales. Last updated 5 months ago.
softwaretranscriptomicspythonspatial-datawrapper
3 stars 4.76 score 16 scripts
annennenne
causalDisco:Tools for Causal Discovery on Observational Data
Various tools for inferring causal models from observational data. The package includes an implementation of the temporal Peter-Clark (TPC) algorithm. Petersen, Osler and Ekstrøm (2021) <doi:10.1093/aje/kwab087>. It also includes general tools for evaluating differences in adjacency matrices, which can be used for evaluating performance of causal discovery procedures.
Maintained by Anne Helby Petersen. Last updated 27 days ago.
19 stars 4.76 score 10 scriptsbioc
spoon:Address the Mean-variance Relationship in Spatial Transcriptomics Data
This package addresses the mean-variance relationship in spatially resolved transcriptomics data. Precision weights are generated for individual observations using Empirical Bayes techniques. These weights are used to rescale the data and covariates, which are then used as input in spatially variable gene detection tools.
Maintained by Kinnary Shah. Last updated 11 days ago.
spatialsinglecelltranscriptomicsgeneexpressionpreprocessing
4.76 score 19 scripts
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.
fluencyimage-analysisimage-analytics
10 stars 4.70 score 9 scriptsbioc
smoothclust:smoothclust
Method for segmentation of spatial domains and spatially-aware clustering in spatial transcriptomics data. The method generates spatial domains with smooth boundaries by smoothing gene expression profiles across neighboring spatial locations, followed by unsupervised clustering. Spatial domains consisting of consistent mixtures of cell types may then be further investigated by applying cell type compositional analyses or differential analyses.
Maintained by Lukas M. Weber. Last updated 7 days ago.
spatialsinglecelltranscriptomicsgeneexpressionclustering
1 stars 4.70 score 7 scriptsropensci
MtreeRing:A Shiny Application for Automatic Measurements of Tree-Ring Widths on Digital Images
Use morphological image processing and edge detection algorithms to automatically measure tree ring widths on digital images. Users can also manually mark tree rings on species with complex anatomical structures. The arcs of inner-rings and angles of successive inclined ring boundaries are used to correct ring-width series. The package provides a Shiny-based application, allowing R beginners to easily analyze tree ring images and export ring-width series in standard file formats.
Maintained by Jingning Shi. Last updated 9 months ago.
dendrochronologyforestforestryshiny-appsshinyapptree-ring-widthtree-rings
33 stars 4.66 score 14 scripts
luigi-annic
WorldMapR:Worldwide or Coordinates-Based Heat Maps
Easily plot heat maps of the world, based on continuous or categorical data. Country labels can also be added to the map.
Maintained by Luigi Annicchiarico. Last updated 9 days ago.
4.65 score 2 scriptsloelschlaeger
optimizeR:Unified Framework for Numerical Optimizers
Provides a unified object-oriented framework for numerical optimizers in R. Allows for both minimization and maximization with any optimizer, optimization over more than one function argument, measuring of computation time, setting a time limit for long optimization tasks.
Maintained by Lennart Oelschläger. Last updated 3 days ago.
4 stars 4.62 score 7 scripts 1 dependents
telfer
pressuRe:Imports, Processes, and Visualizes Biomechanical Pressure Data
Allows biomechanical pressure data from a range of systems to be imported and processed in a reproducible manner. Automatic and manual tools are included to let the user define regions (masks) to be analyzed. Also includes functions for visualizing and animating pressure data. Example methods are described in Shi et al., (2022) <doi:10.1038/s41598-022-19814-0>, Lee et al., (2014) <doi:10.1186/1757-1146-7-18>, van der Zward et al., (2014) <doi:10.1186/1757-1146-7-20>, Najafi et al., (2010) <doi:10.1016/j.gaitpost.2009.09.003>, Cavanagh and Rodgers (1987) <doi:10.1016/0021-9290(87)90255-7>.
Maintained by Scott Telfer. Last updated 6 days ago.
2 stars 4.62 scorebioc
stJoincount:stJoincount - Join count statistic for quantifying spatial correlation between clusters
stJoincount facilitates the application of join count analysis to spatial transcriptomic data generated from the 10x Genomics Visium platform. This tool first converts a labeled spatial tissue map into a raster object, in which each spatial feature is represented by a pixel coded by label assignment. This process includes automatic calculation of optimal raster resolution and extent for the sample. A neighbors list is then created from the rasterized sample, in which adjacent and diagonal neighbors for each pixel are identified. After adding binary spatial weights to the neighbors list, a multi-categorical join count analysis is performed to tabulate "joins" between all possible combinations of label pairs. The function returns the observed join counts, the expected count under conditions of spatial randomness, and the variance calculated under non-free sampling. The z-score is then calculated as the difference between observed and expected counts, divided by the square root of the variance.
Maintained by Jiarong Song. Last updated 5 months ago.
transcriptomicsclusteringspatialbiocviewssoftware
4 stars 4.60 score 3 scriptsbioc
CARDspa:Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics
CARD is a reference-based deconvolution method that estimates cell type composition in spatial transcriptomics based on cell type specific expression information obtained from a reference scRNA-seq data. A key feature of CARD is its ability to accommodate spatial correlation in the cell type composition across tissue locations, enabling accurate and spatially informed cell type deconvolution as well as refined spatial map construction. CARD relies on an efficient optimization algorithm for constrained maximum likelihood estimation and is scalable to spatial transcriptomics with tens of thousands of spatial locations and tens of thousands of genes.
Maintained by Jing Fu. Last updated 3 days ago.
spatialsinglecelltranscriptomicsvisualizationopenblascppopenmp
4.60 score 3 scripts
davidcarayon
IDEATools:Individual and Group Farm Sustainability Assessments using the IDEA4 Method
Collection of tools to automate the processing of data collected though the IDEA4 method (see Zahm et al. (2018) <doi:10.1051/cagri/2019004> ). Starting from the original data collecting files this packages provides functions to compute IDEA indicators, draw modern and aesthetic plots, and produce a wide range of reporting materials.
Maintained by David Carayon. Last updated 10 months ago.
1 stars 4.59 score 26 scripts
ggseg
ggsegExtra:Extra Utilities for the 'ggseg' and 'ggseg3d' Plotting Tools
Contains functions to create new data sets compatible with the 'ggseg' and 'ggseg3d' packages for plotting brain segmentations through R. Requires several external software to be installed on the system for atlas creations to work, and most of these are not available for windows. But atlas creation tools exist for 2d simple features data, and also 3d tri-surface mesh plots. Also has a list of compatible data sets and functions for easy installation of these.
Maintained by Athanasia Mo Mowinckel. Last updated 3 years ago.
55 stars 4.59 score 70 scriptsbioc
BioGA:Bioinformatics Genetic Algorithm (BioGA)
Genetic algorithm are a class of optimization algorithms inspired by the process of natural selection and genetics. This package allows users to analyze and optimize high throughput genomic data using genetic algorithms. The functions provided are implemented in C++ for improved speed and efficiency, with an easy-to-use interface for use within R.
Maintained by Dany Mukesha. Last updated 5 months ago.
experimentaldesigntechnologygenetic-algorithmoptimizationcpp
4.54 score 5 scriptsjonocarroll
ggghost:Capture the Spirit of Your 'ggplot2' Calls
Creates a reproducible 'ggplot2' object by storing the data and calls.
Maintained by Jonathan Carroll. Last updated 7 years ago.
ggplot2plottingvisualisationvisualization
50 stars 4.54 score 14 scripts
learnitr
learnitdown:R Markdown, Bookdown and Learnr Additions for Learning Material
Extension to R Markdown, Bookdown and Learnr for building better learning and e-learning material: H5P integration, course-contextual divs, differed loading of Shiny and learnr applications, and much more ...
Maintained by Philippe Grosjean. Last updated 7 months ago.
bookdownlearning-resourcesr-markdownteaching-materials
13 stars 4.49 score 16 scriptsbioc
xenLite:Simple classes and methods for managing Xenium datasets
Define a relatively light class for managing Xenium data using Bioconductor. Address use of parquet for coordinates, SpatialExperiment for assay and sample data. Address serialization and use of cloud storage.
Maintained by Vincent Carey. Last updated 5 months ago.
1 stars 4.48 score 4 scripts
sammo3182
drhutools:Political Science Academic Research Gears
Using these tools to simplify the research process of political science and other social sciences. The current version can create folder system for academic project in political science, calculate psychological trait scores, visualize experimental and spatial data, and set up color-blind palette, functions used in academic research of political psychology or political science in general.
Maintained by Yue Hu. Last updated 3 months ago.
2 stars 4.45 score 3 scripts
bioc
XeniumIO:Import and represent Xenium data from the 10X Xenium Analyzer
The package allows users to readily import spatial data obtained from the 10X Xenium Analyzer pipeline. Supported formats include 'parquet', 'h5', and 'mtx' files. The package mainly represents data as SpatialExperiment objects.
Maintained by Marcel Ramos. Last updated 2 months ago.
softwareinfrastructuredataimportsinglecellspatialu24ca289073
4.40 score 2 scripts
the-hull
datacleanr:Interactive and Reproducible Data Cleaning
Flexible and efficient cleaning of data with interactivity. 'datacleanr' facilitates best practices in data analyses and reproducibility with built-in features and by translating interactive/manual operations to code. The package is designed for interoperability, and so seamlessly fits into reproducible analyses pipelines in 'R'.
Maintained by Alexander Hurley. Last updated 3 years ago.
annotation-tooldata-cleaningoutlier-detectionoutlier-removalreproducibility
20 stars 4.38 score 24 scriptsbioc
CTSV:Identification of cell-type-specific spatially variable genes accounting for excess zeros
The R package CTSV implements the CTSV approach developed by Jinge Yu and Xiangyu Luo that detects cell-type-specific spatially variable genes accounting for excess zeros. CTSV directly models sparse raw count data through a zero-inflated negative binomial regression model, incorporates cell-type proportions, and performs hypothesis testing based on R package pscl. The package outputs p-values and q-values for genes in each cell type, and CTSV is scalable to datasets with tens of thousands of genes measured on hundreds of spots. CTSV can be installed in Windows, Linux, and Mac OS.
Maintained by Jinge Yu Developer. Last updated 5 months ago.
geneexpressionstatisticalmethodregressionspatialgenetics
2 stars 4.38 score 12 scripts
bioc
tpSVG:Thin plate models to detect spatially variable genes
The goal of `tpSVG` is to detect and visualize spatial variation in the gene expression for spatially resolved transcriptomics data analysis. Specifically, `tpSVG` introduces a family of count-based models, with generalizable parametric assumptions such as Poisson distribution or negative binomial distribution. In addition, comparing to currently available count-based model for spatially resolved data analysis, the `tpSVG` models improves computational time, and hence greatly improves the applicability of count-based models in SRT data analysis.
Maintained by Boyi Guo. Last updated 5 months ago.
spatialtranscriptomicsgeneexpressionsoftwarestatisticalmethoddimensionreductionregressionpreprocessingspatially-resolvespatially-variable-genes
2 stars 4.30 score 2 scriptsbioc
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.
geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsproprietaryplatformsrnaseqspatialdatarepresentationvisualizationopenjdk
4.30 score 8 scripts
jiaxiangbu
add2ggplot:Add to 'ggplot2'
Create 'ggplot2' themes and color palettes.
Maintained by Jiaxiang Li. Last updated 5 years ago.
4 stars 4.30 score 8 scripts
luisdva
hexsession:Create a tile of logos for loaded packages
Creates a responsive HTML file with tiled hex logos for all loaded packages in a session, which can be saved as a static screenshot in png format.
Maintained by Luis D. Verde Arregoitia. Last updated 2 months ago.
35 stars 4.20 score 4 scripts
yingjie4science
SDGdetector:Detect SDGs and Targets in Text
Identify 17 Sustainable Development Goals and associated 169 targets in text.
Maintained by Yingjie Li. Last updated 6 months ago.
sdgsdgssustainabilitysustainable-development-goalstext-mining
15 stars 4.18 score 10 scriptsbioc
spatialSimGP:Simulate Spatial Transcriptomics Data with the Mean-variance Relationship
This packages simulates spatial transcriptomics data with the mean- variance relationship using a Gaussian Process model per gene.
Maintained by Kinnary Shah. Last updated 5 months ago.
spatialtranscriptomicsgeneexpression
4.18 score 2 scriptsbioc
tomoseqr:R Package for Analyzing Tomo-seq Data
`tomoseqr` is an R package for analyzing Tomo-seq data. Tomo-seq is a genome-wide RNA tomography method that combines combining high-throughput RNA sequencing with cryosectioning for spatially resolved transcriptomics. `tomoseqr` reconstructs 3D expression patterns from tomo-seq data and visualizes the reconstructed 3D expression patterns.
Maintained by Ryosuke Matsuzawa. Last updated 5 months ago.
geneexpressionsequencingrnaseqtranscriptomicsspatialvisualizationsoftware
4.18 score 15 scripts
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.
21 stars 4.17 score 14 scripts
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.
21 stars 4.02 score 3 scriptsbioc
DESpace:DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions
Intuitive framework for identifying spatially variable genes (SVGs) and differential spatial variable pattern (DSP) between conditions via edgeR, a popular method for performing differential expression analyses. Based on pre-annotated spatial clusters as summarized spatial information, DESpace models gene expression using a negative binomial (NB), via edgeR, with spatial clusters as covariates. SVGs are then identified by testing the significance of spatial clusters. For multi-sample, multi-condition datasets, we again fit a NB model via edgeR, incorporating spatial clusters, conditions and their interactions as covariates. DSP genes-representing differences in spatial gene expression patterns across experimental conditions-are identified by testing the interaction between spatial clusters and conditions.
Maintained by Peiying Cai. Last updated 2 days ago.
spatialsinglecellrnaseqtranscriptomicsgeneexpressionsequencingdifferentialexpressionstatisticalmethodvisualization
4 stars 4.02 score 13 scriptsbioc
seqArchRplus:Downstream analyses of promoter sequence architectures and HTML report generation
seqArchRplus facilitates downstream analyses of promoter sequence architectures/clusters identified by seqArchR (or any other tool/method). With additional available information such as the TPM values and interquantile widths (IQWs) of the CAGE tag clusters, seqArchRplus can order the input promoter clusters by their shape (IQWs), and write the cluster information as browser/IGV track files. Provided visualizations are of two kind: per sample/stage and per cluster visualizations. Those of the first kind include: plot panels for each sample showing per cluster shape, TPM and other score distributions, sequence logos, and peak annotations. The second include per cluster chromosome-wise and strand distributions, motif occurrence heatmaps and GO term enrichments. Additionally, seqArchRplus can also generate HTML reports for easy viewing and comparison of promoter architectures between samples/stages.
Maintained by Sarvesh Nikumbh. Last updated 5 months ago.
annotationvisualizationreportwritinggomotifannotationclustering
1 stars 4.00 score 2 scripts
archaeothommy
chronochrt:Creating Chronological Charts
Easy way to draw chronological charts from tables, aiming to include an intuitive environment for anyone new to R. Includes 'ggplot2' geoms and theme for chronological charts.
Maintained by Thomas Rose. Last updated 6 months ago.
4.00 score 6 scripts
hanjunwei-lab
SMDIC:Identification of Somatic Mutation-Driven Immune Cells
A computing tool is developed to automated identify somatic mutation-driven immune cells. The operation modes including: i) inferring the relative abundance matrix of tumor-infiltrating immune cells and integrating it with a particular gene mutation status, ii) detecting differential immune cells with respect to the gene mutation status and converting the abundance matrix of significant differential immune cell into two binary matrices (one for up-regulated and one for down-regulated), iii) identifying somatic mutation-driven immune cells by comparing the gene mutation status with each immune cell in the binary matrices across all samples, and iv) visualization of immune cell abundance of samples in different mutation status..
Maintained by Junwei Han. Last updated 5 months ago.
2 stars 4.00 score 5 scripts
josesamos
moodef:Defining 'Moodle' Elements from R
The main objective of this package is to support the definition of 'Moodle' elements taking advantage of the power that R offers. In this first version, it allows the definition of quizzes to be included in the question bank.
Maintained by Jose Samos. Last updated 2 months ago.
1 stars 4.00 score 4 scriptsbioc
octad:Open Cancer TherApeutic Discovery (OCTAD)
OCTAD provides a platform for virtually screening compounds targeting precise cancer patient groups. The essential idea is to identify drugs that reverse the gene expression signature of disease by tamping down over-expressed genes and stimulating weakly expressed ones. The package offers deep-learning based reference tissue selection, disease gene expression signature creation, pathway enrichment analysis, drug reversal potency scoring, cancer cell line selection, drug enrichment analysis and in silico hit validation. It currently covers ~20,000 patient tissue samples covering 50 cancer types, and expression profiles for ~12,000 distinct compounds.
Maintained by E. Chekalin. Last updated 5 months ago.
classificationgeneexpressionpharmacogeneticspharmacogenomicssoftwaregenesetenrichment
4.00 score 4 scriptsbioc
alabaster:Umbrella for the Alabaster Framework
Umbrella for the alabaster suite, providing a single-line import for all alabaster.* packages. Installing this package ensures that all known alabaster.* packages are also installed, avoiding problems with missing packages when a staging method or loading function is dynamically requested. Obviously, this comes at the cost of needing to install more packages, so advanced users and application developers may prefer to install the required alabaster.* packages individually.
Maintained by Aaron Lun. Last updated 5 months ago.
4.00 score 3 scriptsbioc
OMICsPCA:An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples
OMICsPCA is an analysis pipeline designed to integrate multi OMICs experiments done on various subjects (e.g. Cell lines, individuals), treatments (e.g. disease/control) or time points and to analyse such integrated data from various various angles and perspectives. In it's core OMICsPCA uses Principal Component Analysis (PCA) to integrate multiomics experiments from various sources and thus has ability to over data insufficiency issues by using the ingegrated data as representatives. OMICsPCA can be used in various application including analysis of overall distribution of OMICs assays across various samples /individuals /time points; grouping assays by user-defined conditions; identification of source of variation, similarity/dissimilarity between assays, variables or individuals.
Maintained by Subhadeep Das. Last updated 5 months ago.
immunooncologymultiplecomparisonprincipalcomponentdatarepresentationworkflowvisualizationdimensionreductionclusteringbiologicalquestionepigeneticsworkflowtranscriptiongeneticvariabilityguibiomedicalinformaticsepigeneticsfunctionalgenomicssinglecell
4.00 score 1 scriptsbioc
ExperimentSubset:Manages subsets of data with Bioconductor Experiment objects
Experiment objects such as the SummarizedExperiment or SingleCellExperiment are data containers for one or more matrix-like assays along with the associated row and column data. Often only a subset of the original data is needed for down-stream analysis. For example, filtering out poor quality samples will require excluding some columns before analysis. The ExperimentSubset object is a container to efficiently manage different subsets of the same data without having to make separate objects for each new subset.
Maintained by Irzam Sarfraz. Last updated 5 months ago.
infrastructuresoftwaredataimportdatarepresentation
4.00 score 8 scripts
simonliles
protein8k:Perform Analysis and Create Visualizations of Proteins
Read Protein Data Bank (PDB) files, performs its analysis, and presents the result using different visualization types including 3D. The package also has additional capability for handling Virus Report data from the National Center for Biotechnology Information (NCBI) database.
Maintained by Simon Liles. Last updated 4 years ago.
1 stars 4.00 score 4 scripts
juananvg
GSEMA:Gene Set Enrichment Meta-Analysis
Performing the different steps of gene set enrichment meta-analysis. It provides different functions that allow the application of meta-analysis based on the combination of effect sizes from different pathways in different studies to obtain significant pathways that are common to all of them.
Maintained by Juan Antonio Villatoro-García. Last updated 6 months ago.
statisticalmethodgenesetenrichmentpathways
3.90 score 3 scripts
mpallocc
autoGO:Auto-GO: Reproducible, Robust and High Quality Ontology Enrichment Visualizations
Auto-GO is a framework that enables automated, high quality Gene Ontology enrichment analysis visualizations. It also features a handy wrapper for Differential Expression analysis around the 'DESeq2' package described in Love et al. (2014) <doi:10.1186/s13059-014-0550-8>. The whole framework is structured in different, independent functions, in order to let the user decide which steps of the analysis to perform and which plot to produce.
Maintained by Fabio Ticconi. Last updated 1 months ago.
2 stars 3.90 score
marcohlmann
metanetwork:Handling and Representing Trophic Networks in Space and Time
A toolbox to handle and represent trophic networks in space or time across aggregation levels. This package contains a layout algorithm specifically designed for trophic networks, using dimension reduction on a diffusion graph kernel and trophic levels. Importantly, this package provides a layout method applicable for large trophic networks. The package also implements network diversity indices at different aggregation levels and connectance computation.
Maintained by Marc Ohlmann. Last updated 2 years ago.
2 stars 3.89 score 77 scripts
csafe-isu
handwriterApp:A 'shiny' Application for Handwriting Analysis
Perform statistical writership analysis of scanned handwritten documents with a 'shiny' app for 'handwriter'.
Maintained by Stephanie Reinders. Last updated 4 months ago.
1 stars 3.85 score 9 scripts
shotaochi
magickGUI:GUI Tools for Interactive Image Processing with 'magick'
Enables us to use the functions of the package 'magick' interactively.
Maintained by Shota Ochi. Last updated 2 years ago.
9 stars 3.83 score 15 scripts
guokai8
eoffice:Export or Graph and Tables to 'Microsoft' Office and Import Figures and Tables
Provides wrap functions to export and import graphics and data frames in R to 'microsoft' office. And This package also provide write out figures with lots of different formats. Since people may work on the platform without GUI support, the package also provide function to easily write out figures to lots of different type of formats. Now this package provide function to extract colors from all types of figures and pdf files.
Maintained by Kai Guo. Last updated 2 years ago.
1 stars 3.80 score 100 scripts
carloshellin
LearningRlab:Statistical Learning Functions
Aids in learning statistical functions incorporating the result of calculus done with each function and how they are obtained, that is, which equation and variables are used. Also for all these equations and their related variables detailed explanations and interactive exercises are also included. All these characteristics allow to the package user to improve the learning of statistics basics by means of their use.
Maintained by Carlos Javier Hellin Asensio. Last updated 2 years ago.
3.64 score 44 scripts
asa12138
plot4fun:Just Plot for Fun
Explore the world of R graphics with fun and interesting plot functions! Use make_LED() to create dynamic LED screens, draw interconnected rings with Olympic_rings(), and make festive Chinese couplets with chunlian(). Unleash your creativity and turn data into exciting visuals!
Maintained by Chen Peng. Last updated 5 months ago.
2 stars 3.60 score 1 scripts
fmmattioni
metabolic:Datasets and Functions for Reproducing Meta-Analyses
Dataset and functions from the meta-analysis published in Medicine & Science in Sports & Exercise. It contains all the data and functions to reproduce the analysis. "Effectiveness of HIIE versus MICT in Improving Cardiometabolic Risk Factors in Health and Disease: A Meta-analysis". Felipe Mattioni Maturana, Peter Martus, Stephan Zipfel, Andreas M Nieß (2020) <doi:10.1249/MSS.0000000000002506>.
Maintained by Felipe Mattioni Maturana. Last updated 1 years ago.
8 stars 3.60 score 8 scripts
gofigr
gofigR:Client for 'GoFigr.io'
Integrates with your 'RMarkdown' documents to automatically publish figures to the <https://GoFigr.io> service. Supports both 'knitr' and interactive execution within 'RStudio'.
Maintained by Maciej Pacula. Last updated 11 days ago.
3.48 score
cran
multipanelfigure:Infrastructure to Assemble Multi-Panel Figures (from Grobs)
Tools to create a layout for figures made of multiple panels, and to fill the panels with base, 'lattice', 'ggplot2' and 'ComplexHeatmap' plots, grobs, as well as content from all image formats supported by 'ImageMagick' (accessed through 'magick').
Maintained by Johannes Graumann. Last updated 12 months ago.
3 stars 3.48 scorebioc
OpenStats:A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association
Package contains several methods for statistical analysis of genotype to phenotype association in high-throughput screening pipelines.
Maintained by Marina Kan. Last updated 4 months ago.
statisticalmethodbatcheffectbayesian
3.48 score 4 scripts
paithiov909
shikakusphere:Miscellaneous Functions for Japanese Mahjong
A collection of miscellaneous functions for Japanese mahjong that wraps C++ sources of 'shanten-number' <https://github.com/tomohxx/shanten-number> and 'cmajiang' <https://github.com/TadaoYamaoka/cmajiang>.
Maintained by Akiru Kato. Last updated 29 days ago.
4 stars 3.41 score 5 scriptsdjnavarro
rainbowr:Make LGBT Hexes and Flags
Generates a variety of LGBT flags (e.g., rainbow, transgender) overlaid with the R logo, using the magick package. Also generates hex stickers based on LGBT flags and tilings thereof.
Maintained by Danielle Navarro. Last updated 5 years ago.
23 stars 3.40 score 22 scriptscran
convevol:Analysis of Convergent Evolution
Quantifies and assesses the significance of convergent evolution using multiple methods and measures as described in Stayton (2015) <DOI: 10.1111/evo.12729> and Grossnickle et al. 2023. Also displays results in various ways.
Maintained by C. Tristan Stayton. Last updated 8 months ago.
3.30 score
milesmcbain
inlegend:Inset legend themes for ggplot2 maps
Provides themes for making ggplot2 maps with inset legends and without whitespace around the margins.
Maintained by Miles McBain. Last updated 4 years ago.
40 stars 3.30 score 7 scriptsbioc
oppar:Outlier profile and pathway analysis in R
The R implementation of mCOPA package published by Wang et al. (2012). Oppar provides methods for Cancer Outlier profile Analysis. Although initially developed to detect outlier genes in cancer studies, methods presented in oppar can be used for outlier profile analysis in general. In addition, tools are provided for gene set enrichment and pathway analysis.
Maintained by Soroor Hediyeh zadeh. Last updated 5 months ago.
pathwaysgenesetenrichmentsystemsbiologygeneexpressionsoftware
3.30 score 3 scripts
pratheesh3780
grapesAgri1:Collection of Shiny Apps for Agricultural Research Data Analysis
Allows user to have graphical user interface to perform analysis of Agricultural experimental data. On using the functions in this package a Interactive User Interface will pop up. Apps Works by simple upload of files in CSV format.
Maintained by Pratheesh P. Gopinath. Last updated 1 years ago.
1 stars 3.30 score 3 scriptscran
zoomGroupStats:Analyze Text, Audio, and Video from 'Zoom' Meetings
Provides utilities for processing and analyzing the files that are exported from a recorded 'Zoom' Meeting. This includes analyzing data captured through video cameras and microphones, the text-based chat, and meta-data. You can analyze aspects of the conversation among meeting participants and their emotional expressions throughout the meeting.
Maintained by Andrew Knight. Last updated 4 years ago.
3.30 scorebioc
rfaRm:An R interface to the Rfam database
rfaRm provides a client interface to the Rfam database of RNA families. Data that can be retrieved include RNA families, secondary structure images, covariance models, sequences within each family, alignments leading to the identification of a family and secondary structures in the dot-bracket format.
Maintained by Lara Selles Vidal. Last updated 5 months ago.
functionalgenomicsdataimportthirdpartyclientvisualizationmultiplesequencealignment
3.30 score 1 scripts
andriyprotsak5
UAHDataScienceSF:Interactive Statistical Learning Functions
An educational toolkit for learning statistical concepts through interactive exploration. Provides functions for basic statistics (mean, variance, etc.) and probability distributions with step-by-step explanations and interactive learning modes. Each function can be used for simple calculations, detailed learning with explanations, or interactive practice with feedback.
Maintained by Andriy Protsak Protsak. Last updated 1 months ago.
3.30 score