Showing 158 of total 158 results (show query)
hafen
geofacet:'ggplot2' Faceting Utilities for Geographical Data
Provides geographical faceting functionality for 'ggplot2'. Geographical faceting arranges a sequence of plots of data for different geographical entities into a grid that preserves some of the geographical orientation.
Maintained by Ryan Hafen. Last updated 7 months ago.
319.5 match 340 stars 9.78 score 1.5k scripts 4 dependents
r-spatial
sf:Simple Features for R
Support for simple feature access, a standardized way to encode and analyze spatial vector data. Binds to 'GDAL' <doi: 10.5281/zenodo.5884351> for reading and writing data, to 'GEOS' <doi: 10.5281/zenodo.11396894> for geometrical operations, and to 'PROJ' <doi: 10.5281/zenodo.5884394> for projection conversions and datum transformations. Uses by default the 's2' package for geometry operations on geodetic (long/lat degree) coordinates.
Maintained by Edzer Pebesma. Last updated 15 days ago.
31.8 match 1.4k stars 22.42 score 117k scripts 1.2k dependents
bioc
GEOquery:Get data from NCBI Gene Expression Omnibus (GEO)
The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.
Maintained by Sean Davis. Last updated 5 months ago.
microarraydataimportonechanneltwochannelsagebioconductorbioinformaticsdata-sciencegenomicsncbi-geo
39.2 match 92 stars 14.46 score 4.1k scripts 44 dependents
rspatial
terra:Spatial Data Analysis
Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Maintained by Robert J. Hijmans. Last updated 9 hours ago.
geospatialrasterspatialvectoronetbbprojgdalgeoscpp
30.0 match 559 stars 17.65 score 17k scripts 849 dependents
paleolimbot
geos:Open Source Geometry Engine ('GEOS') R API
Provides an R API to the Open Source Geometry Engine ('GEOS') library (<https://libgeos.org/>) and a vector format with which to efficiently store 'GEOS' geometries. High-performance functions to extract information from, calculate relationships between, and transform geometries are provided. Finally, facilities to import and export geometry vectors to other spatial formats are provided.
Maintained by Dewey Dunnington. Last updated 1 years ago.
67.0 match 62 stars 7.63 score 110 scripts 8 dependentsr-spatial
lwgeom:Bindings to Selected 'liblwgeom' Functions for Simple Features
Access to selected functions found in 'liblwgeom' <https://github.com/postgis/postgis/tree/master/liblwgeom>, the light-weight geometry library used by 'PostGIS' <http://postgis.net/>.
Maintained by Edzer Pebesma. Last updated 1 months ago.
30.0 match 61 stars 12.95 score 1.7k scripts 66 dependents
rnuske
apcf:Adapted Pair Correlation Function
The adapted pair correlation function transfers the concept of the pair correlation function from point patterns to patterns of objects of finite size and irregular shape (e.g. lakes within a country). The pair correlation function describes the spatial distribution of objects, e.g. random, aggregated or regularly spaced. This is a reimplementation of the method suggested by Nuske et al. (2009) <doi:10.1016/j.foreco.2009.09.050> using the library 'GEOS' <doi:10.5281/zenodo.11396894>.
Maintained by Robert Nuske. Last updated 10 days ago.
geogeospoint-pattern-analysisspatial-statisticscpp
41.5 match 5 stars 4.95 score 12 scripts
r-barnes
dggridR:Discrete Global Grids
Spatial analyses involving binning require that every bin have the same area, but this is impossible using a rectangular grid laid over the Earth or over any projection of the Earth. Discrete global grids use hexagons, triangles, and diamonds to overcome this issue, overlaying the Earth with equally-sized bins. This package provides utilities for working with discrete global grids, along with utilities to aid in plotting such data.
Maintained by Sebastian Krantz. Last updated 6 months ago.
discrete-global-gridsgeospatialspatial-analysiscpp
21.8 match 168 stars 9.37 score 388 scripts 1 dependents
grundy95
changepoint.geo:Geometrically Inspired Multivariate Changepoint Detection
Implements the high-dimensional changepoint detection method GeomCP and the related mappings used for changepoint detection. These methods view the changepoint problem from a geometrical viewpoint and aim to extract relevant geometrical features in order to detect changepoints. The geomcp() function should be your first point of call. References: Grundy et al. (2020) <doi:10.1007/s11222-020-09940-y>.
Maintained by Thomas Grundy. Last updated 4 years ago.
39.2 match 11 stars 4.74 score 10 scripts
ropensci
osmextract:Download and Import Open Street Map Data Extracts
Match, download, convert and import Open Street Map data extracts obtained from several providers.
Maintained by Andrea Gilardi. Last updated 2 months ago.
geogeofabrik-zoneopen-dataosmosm-pbf
11.0 match 173 stars 9.73 score 342 scripts
eglenn
acs:Download, Manipulate, and Present American Community Survey and Decennial Data from the US Census
Provides a general toolkit for downloading, managing, analyzing, and presenting data from the U.S. Census (<https://www.census.gov/data/developers/data-sets.html>), including SF1 (Decennial short-form), SF3 (Decennial long-form), and the American Community Survey (ACS). Confidence intervals provided with ACS data are converted to standard errors to be bundled with estimates in complex acs objects. Package provides new methods to conduct standard operations on acs objects and present/plot data in statistically appropriate ways.
Maintained by Ezra Haber Glenn. Last updated 6 years ago.
19.2 match 10 stars 5.42 score 430 scripts 3 dependentsropensci
parzer:Parse Messy Geographic Coordinates
Parse messy geographic coordinates from various character formats to decimal degree numeric values. Parse coordinates into their parts (degree, minutes, seconds); calculate hemisphere from coordinates; pull out individually degrees, minutes, or seconds; add and subtract degrees, minutes, and seconds. C++ code herein originally inspired from code written by Jeffrey D. Bogan, but then completely re-written.
Maintained by Alban Sagouis. Last updated 1 months ago.
geospatialdatalatitudelongitudeparsercoordinatesgeocpp
11.0 match 65 stars 8.45 score 162 scripts 3 dependentsbioc
GeoTcgaData:Processing Various Types of Data on GEO and TCGA
Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It's easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.
Maintained by Erqiang Hu. Last updated 5 months ago.
geneexpressiondifferentialexpressionrnaseqcopynumbervariationmicroarraysoftwarednamethylationdifferentialmethylationsnpatacseqmethylationarray
15.4 match 25 stars 5.85 score 19 scripts
mages
googleVis:R Interface to Google Charts
R interface to Google's chart tools, allowing users to create interactive charts based on data frames. Charts are displayed locally via the R HTTP help server. A modern browser with an Internet connection is required. The data remains local and is not uploaded to Google.
Maintained by Markus Gesmann. Last updated 10 months ago.
6.6 match 361 stars 12.98 score 2.4k scripts 11 dependents
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
11.5 match 17 stars 7.29 score 60 scriptsbioc
GEOfastq:Downloads ENA Fastqs With GEO Accessions
GEOfastq is used to download fastq files from the European Nucleotide Archive (ENA) starting with an accession from the Gene Expression Omnibus (GEO). To do this, sample metadata is retrieved from GEO and the Sequence Read Archive (SRA). SRA run accessions are then used to construct FTP and aspera download links for fastq files generated by the ENA.
Maintained by Alex Pickering. Last updated 5 months ago.
rnaseqdataimportbioinformaticsfastqgene-expressiongeorna-seq
16.7 match 4 stars 4.60 score 6 scripts
politicaargentina
geoAr:Argentina's Spatial Data Toolbox
Collection of tools that facilitates data access and workflow for spatial analysis of Argentina. Includes historical information from censuses, administrative limits at different levels of aggregation, location of human settlements, among others. Since it is expected that the majority of users will be Spanish-speaking, the documentation of the package prioritizes this language, although an effort is made to also offer annotations in English.
Maintained by Juan Pablo Ruiz Nicolini. Last updated 1 years ago.
11.0 match 15 stars 6.55 score 78 scripts
evolecolgroup
geoGraph:Walking through the geographic space using graphs
Classes and methods for spatial graphs interfaced with support for GIS shapefiles.
Maintained by Andrea Manica. Last updated 8 days ago.
21.8 match 4 stars 3.30 score 2 scripts
crunch-io
crunch:Crunch.io Data Tools
The Crunch.io service <https://crunch.io/> provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
Maintained by Greg Freedman Ellis. Last updated 9 days ago.
6.3 match 9 stars 10.53 score 200 scripts 2 dependents
johncoene
echarts4r:Create Interactive Graphs with 'Echarts JavaScript' Version 5
Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes 36 chart types, themes, 'Shiny' proxies and animations.
Maintained by David Munoz Tord. Last updated 1 days ago.
echartshacktoberfesthtmlwidgethtmlwidgetsvisualization
5.6 match 603 stars 11.45 score 1.3k scripts 11 dependents
geo-sapiens
RColetum:Access your Coletum's Data from API
Get your data (forms, structures, answers) from Coletum <https://coletum.com> to handle and analyse.
Maintained by Andrรฉ Smaniotto. Last updated 2 years ago.
15.0 match 7 stars 4.02 score 8 scriptsr-spatial
mapedit:Interactive Editing of Spatial Data in R
Suite of interactive functions and helpers for selecting and editing geospatial data.
Maintained by Tim Appelhans. Last updated 3 years ago.
7.0 match 218 stars 8.20 score 410 scripts 1 dependentsbioc
phantasus:Visual and interactive gene expression analysis
Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus โ a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.
Maintained by Alexey Sergushichev. Last updated 5 months ago.
geneexpressionguivisualizationdatarepresentationtranscriptomicsrnaseqmicroarraynormalizationclusteringdifferentialexpressionprincipalcomponentimmunooncology
7.4 match 43 stars 7.68 score 15 scriptsbioc
ChIPseeker:ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.
Maintained by Guangchuang Yu. Last updated 5 months ago.
annotationchipseqsoftwarevisualizationmultiplecomparisonatac-seqchip-seqcomparisonepigeneticsepigenomics
4.2 match 234 stars 13.02 score 1.6k scripts 5 dependents
oobianom
quickcode:Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to improve your scripts. Improve the quality and reproducibility of 'R' scripts.
Maintained by Obinna Obianom. Last updated 12 days ago.
6.8 match 5 stars 7.76 score 7 scripts 6 dependentsbioc
beadarray:Quality assessment and low-level analysis for Illumina BeadArray data
The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.
Maintained by Mark Dunning. Last updated 5 months ago.
microarrayonechannelqualitycontrolpreprocessing
6.6 match 7.88 score 70 scripts 4 dependentsbioc
recount:Explore and download data from the recount project
Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.
Maintained by Leonardo Collado-Torres. Last updated 3 months ago.
coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportimmunooncologyannotation-agnosticbioconductorcountderfinderdeseq2exongenehumanilluminajunctionrecount
5.2 match 41 stars 9.57 score 498 scripts 3 dependents
samuel-marsh
scCustomize:Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing
Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
Maintained by Samuel Marsh. Last updated 3 months ago.
customizationggplot2scrna-seqseuratsingle-cellsingle-cell-genomicssingle-cell-rna-seqvisualization
5.2 match 242 stars 8.75 score 1.1k scriptsbioc
minfi:Analyze Illumina Infinium DNA methylation arrays
Tools to analyze & visualize Illumina Infinium methylation arrays.
Maintained by Kasper Daniel Hansen. Last updated 4 months ago.
immunooncologydnamethylationdifferentialmethylationepigeneticsmicroarraymethylationarraymultichanneltwochanneldataimportnormalizationpreprocessingqualitycontrol
3.5 match 60 stars 12.83 score 996 scripts 26 dependentsbioc
lumi:BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.
Maintained by Lei Huang. Last updated 5 months ago.
microarrayonechannelpreprocessingdnamethylationqualitycontroltwochannel
6.9 match 6.27 score 294 scripts 5 dependentsbioc
GEOexplorer:GEOexplorer: a webserver for gene expression analysis and visualisation
GEOexplorer is a webserver and R/Bioconductor package and web application that enables users to perform gene expression analysis. The development of GEOexplorer was made possible because of the excellent code provided by GEO2R (https: //www.ncbi.nlm.nih.gov/geo/geo2r/).
Maintained by Guy Hunt. Last updated 5 months ago.
softwaregeneexpressionmrnamicroarraydifferentialexpressionmicroarraymicrornaarraytranscriptomicsrnaseq
7.9 match 5 stars 5.32 score 14 scripts
kenaho1
asbio:A Collection of Statistical Tools for Biologists
Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Maintained by Ken Aho. Last updated 2 months ago.
5.9 match 5 stars 7.09 score 310 scripts 3 dependents
jacekbialek
PriceIndices:Calculating Bilateral and Multilateral Price Indexes
Preparing a scanner data set for price dynamics calculations (data selecting, data classification, data matching, data filtering). Computing bilateral and multilateral indexes. For details on these methods see: Diewert and Fox (2020) <doi:10.1080/07350015.2020.1816176>, Biaลek (2019) <doi:10.2478/jos-2019-0014> or Biaลek (2020) <doi:10.2478/jos-2020-0037>.
Maintained by Jacek Biaลek. Last updated 2 months ago.
6.8 match 11 stars 6.06 score 16 scripts
paleolimbot
libgeos:Open Source Geometry Engine ('GEOS') C API
Provides the Open Source Geometry Engine ('GEOS') as a C API that can be used to write high-performance C and C++ geometry operations using R as an interface. Headers are provided to make linking to and using these functions from C++ code as easy and as safe as possible. This package contains an internal copy of the 'GEOS' library to guarantee the best possible consistency on multiple platforms.
Maintained by Dewey Dunnington. Last updated 1 years ago.
7.2 match 18 stars 5.51 score 2 scripts 9 dependents
jessecambon
tidygeocoder:Geocoding Made Easy
An intuitive interface for getting data from geocoding services.
Maintained by Jesse Cambon. Last updated 4 months ago.
3.3 match 287 stars 11.35 score 1.0k scripts 9 dependents
plotly
plotly:Create Interactive Web Graphics via 'plotly.js'
Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.
Maintained by Carson Sievert. Last updated 3 months ago.
d3jsdata-visualizationggplot2javascriptplotlyshinywebgl
1.9 match 2.6k stars 19.36 score 93k scripts 783 dependents
bioc
Moonlight2R:Identify oncogenes and tumor suppressor genes from omics data
The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). We present an updated version of the R/bioconductor package called MoonlightR, namely Moonlight2R, which returns a list of candidate driver genes for specific cancer types on the basis of omics data integration. The Moonlight framework contains a primary layer where gene expression data and information about biological processes are integrated to predict genes called oncogenic mediators, divided into putative tumor suppressors and putative oncogenes. This is done through functional enrichment analyses, gene regulatory networks and upstream regulator analyses to score the importance of well-known biological processes with respect to the studied cancer type. By evaluating the effect of the oncogenic mediators on biological processes or through random forests, the primary layer predicts two putative roles for the oncogenic mediators: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As gene expression data alone is not enough to explain the deregulation of the genes, a second layer of evidence is needed. We have automated the integration of a secondary mutational layer through new functionalities in Moonlight2R. These functionalities analyze mutations in the cancer cohort and classifies these into driver and passenger mutations using the driver mutation prediction tool, CScape-somatic. Those oncogenic mediators with at least one driver mutation are retained as the driver genes. As a consequence, this methodology does not only identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another) but also helps in elucidating the biological processes underlying their specific roles. In particular, Moonlight2R can be used to discover OCGs and TSGs in the same cancer type. This may for instance help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV). In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments. An additional mechanistic layer evaluates if there are mutations affecting the protein stability of the transcription factors (TFs) of the TSGs and OCGs, as that may have an effect on the expression of the genes.
Maintained by Matteo Tiberti. Last updated 2 months ago.
dnamethylationdifferentialmethylationgeneregulationgeneexpressionmethylationarraydifferentialexpressionpathwaysnetworksurvivalgenesetenrichmentnetworkenrichment
5.0 match 5 stars 6.59 score 43 scripts
rubenfcasal
npsp:Nonparametric Spatial Statistics
Multidimensional nonparametric spatial (spatio-temporal) geostatistics. S3 classes and methods for multidimensional: linear binning, local polynomial kernel regression (spatial trend estimation), density and variogram estimation. Nonparametric methods for simultaneous inference on both spatial trend and variogram functions (for spatial processes). Nonparametric residual kriging (spatial prediction). For details on these methods see, for example, Fernandez-Casal and Francisco-Fernandez (2014) <doi:10.1007/s00477-013-0817-8> or Castillo-Paez et al. (2019) <doi:10.1016/j.csda.2019.01.017>.
Maintained by Ruben Fernandez-Casal. Last updated 4 months ago.
geostatisticsspatial-data-analysisstatisticsfortranopenblas
5.8 match 4 stars 5.71 score 64 scriptsbioc
recountmethylation:Access and analyze public DNA methylation array data compilations
Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina's Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info.
Maintained by Sean K Maden. Last updated 5 months ago.
dnamethylationepigeneticsmicroarraymethylationarrayexperimenthub
5.2 match 9 stars 6.28 score 9 scripts
ropengov
regions:Processing Regional Statistics
Validating sub-national statistical typologies, re-coding across standard typologies of sub-national statistics, and making valid aggregate level imputation, re-aggregation, re-weighting and projection down to lower hierarchical levels to create meaningful data panels and time series.
Maintained by Daniel Antal. Last updated 2 years ago.
observatoryregionsropengovstatistics
3.5 match 12 stars 8.81 score 67 scripts 5 dependents
fumi-github
omicwas:Cell-Type-Specific Association Testing in Bulk Omics Experiments
In bulk epigenome/transcriptome experiments, molecular expression is measured in a tissue, which is a mixture of multiple types of cells. This package tests association of a disease/phenotype with a molecular marker for each cell type. The proportion of cell types in each sample needs to be given as input. The package is applicable to epigenome-wide association study (EWAS) and differential gene expression analysis. Takeuchi and Kato (submitted) "omicwas: cell-type-specific epigenome-wide and transcriptome association study".
Maintained by Fumihiko Takeuchi. Last updated 4 years ago.
7.2 match 4 stars 4.30 score 7 scriptsbioc
MoonlightR:Identify oncogenes and tumor suppressor genes from omics data
Motivation: The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). Results: We present an R/bioconductor package called MoonlightR which returns a list of candidate driver genes for specific cancer types on the basis of TCGA expression data. The method first infers gene regulatory networks and then carries out a functional enrichment analysis (FEA) (implementing an upstream regulator analysis, URA) to score the importance of well-known biological processes with respect to the studied cancer type. Eventually, by means of random forests, MoonlightR predicts two specific roles for the candidate driver genes: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As a consequence, this methodology does not only identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another) but also helps in elucidating the biological processes underlying their specific roles. In particular, MoonlightR can be used to discover OCGs and TSGs in the same cancer type. This may help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV) in breast cancer. In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments.
Maintained by Matteo Tiberti. Last updated 5 months ago.
dnamethylationdifferentialmethylationgeneregulationgeneexpressionmethylationarraydifferentialexpressionpathwaysnetworksurvivalgenesetenrichmentnetworkenrichment
4.5 match 17 stars 6.57 score
dfsp-spirit
freesurferformats:Read and Write 'FreeSurfer' Neuroimaging File Formats
Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' <http://freesurfer.net/> formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.
Maintained by Tim Schรคfer. Last updated 6 months ago.
brainbrain-atlasbrain-surfacescurvdtifileformatsfreesurferlabelmeshmghmrineuroimagingparcellationresearchsurfacevoxel
3.7 match 23 stars 8.07 score 25 scripts 8 dependents
xjsun1221
tinyarray:Expression Data Analysis and Visualization
The Gene Expression Omnibus (<https://www.ncbi.nlm.nih.gov/geo/>) and The Cancer Genome Atlas (<https://portal.gdc.cancer.gov/>) are widely used medical public databases. Our platform integrates routine analysis and visualization tools for expression data to provide concise and intuitive data analysis and presentation.
Maintained by Xiaojie Sun. Last updated 9 months ago.
4.4 match 91 stars 6.67 score 138 scripts
robertmyles
tidygeoRSS:Tidy GeoRSS
In order to easily integrate geoRSS data into analysis, 'tidygeoRSS' parses 'geo' feeds and returns tidy simple features data frames.
Maintained by Robert Myles McDonnell. Last updated 5 years ago.
atom-feedgeo-rssgeojsonrsstidy-data
9.7 match 2 stars 3.00 score 5 scriptsropensci
opentripplanner:Setup and connect to 'OpenTripPlanner'
Setup and connect to 'OpenTripPlanner' (OTP) <http://www.opentripplanner.org/>. OTP is an open source platform for multi-modal and multi-agency journey planning written in 'Java'. The package allows you to manage a local version or connect to remote OTP server to find walking, cycling, driving, or transit routes. This package has been peer-reviewed by rOpenSci (v. 0.2.0.0).
Maintained by Malcolm Morgan. Last updated 3 months ago.
dataisochronesjavaopentripplannerotppublic-transportroutingtransporttransportation-planning
3.3 match 83 stars 8.94 score 147 scriptsbioc
ExiMiR:R functions for the normalization of Exiqon miRNA array data
This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported.
Maintained by Sylvain Gubian. Last updated 5 months ago.
microarrayonechanneltwochannelpreprocessinggeneexpressiontranscription
10.4 match 2.78 score 3 scriptsbioc
STRINGdb:STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment Analysis
The STRINGdb package provides a R interface to the STRING protein-protein interactions database (https://string-db.org).
Maintained by Damian Szklarczyk. Last updated 5 months ago.
3.4 match 8.10 score 344 scripts 8 dependentsbioc
clustifyr:Classifier for Single-cell RNA-seq Using Cell Clusters
Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided to assist cell type assignment.
Maintained by Rui Fu. Last updated 5 months ago.
singlecellannotationsequencingmicroarraygeneexpressionassign-identitiesclustersmarker-genesrna-seqsingle-cell-rna-seq
2.9 match 119 stars 9.63 score 296 scriptsbioc
RnBeads:RnBeads
RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.
Maintained by Fabian Mueller. Last updated 1 months ago.
dnamethylationmethylationarraymethylseqepigeneticsqualitycontrolpreprocessingbatcheffectdifferentialmethylationsequencingcpgislandimmunooncologytwochanneldataimport
3.9 match 6.85 score 169 scripts 1 dependents
mpierrejean
acnr:Annotated Copy-Number Regions
This data package provides SNP array data from different types of copy-number regions. These regions were identified manually by the authors of the package and may be used to generate realistic data sets with known truth.
Maintained by Morgane Pierre-Jean. Last updated 3 years ago.
5.0 match 1 stars 5.23 score 19 scripts 3 dependents
gabferreira
phyloraster:Evolutionary Diversity Metrics for Raster Data
Phylogenetic Diversity (PD, Faith 1992), Evolutionary Distinctiveness (ED, Isaac et al. 2007), Phylogenetic Endemism (PE, Rosauer et al. 2009; Laffan et al. 2016), and Weighted Endemism (WE, Laffan et al. 2016) for presence-absence raster. Faith, D. P. (1992) <doi:10.1016/0006-3207(92)91201-3> Isaac, N. J. et al. (2007) <doi:10.1371/journal.pone.0000296> Laffan, S. W. et al. (2016) <doi:10.1111/2041-210X.12513> Rosauer, D. et al. (2009) <doi:10.1111/j.1365-294X.2009.04311.x>.
Maintained by Gabriela Alves-Ferreira. Last updated 15 days ago.
4.3 match 7 stars 5.66 score 33 scripts
josiahparry
rsgeo:An Interface to Rust's 'geo' Library
An R interface to the GeoRust crates 'geo' and 'geo-types' providing access to geometry primitives and algorithms.
Maintained by Josiah Parry. Last updated 7 months ago.
5.8 match 47 stars 4.09 score 13 scriptsbioc
limma:Linear Models for Microarray and Omics Data
Data analysis, linear models and differential expression for omics data.
Maintained by Gordon Smyth. Last updated 4 days ago.
exonarraygeneexpressiontranscriptionalternativesplicingdifferentialexpressiondifferentialsplicinggenesetenrichmentdataimportbayesianclusteringregressiontimecoursemicroarraymicrornaarraymrnamicroarrayonechannelproprietaryplatformstwochannelsequencingrnaseqbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrolbiomedicalinformaticscellbiologycheminformaticsepigeneticsfunctionalgenomicsgeneticsimmunooncologymetabolomicsproteomicssystemsbiologytranscriptomics
1.7 match 13.81 score 16k scripts 585 dependents
cran
rsatscan:Tools, Classes, and Methods for Interfacing with 'SaTScan' Stand-Alone Software
'SaTScan'(TM) <https://www.satscan.org> is software for finding regions in Time, Space, or Time-Space that have excess risk, based on scan statistics, and uses Monte Carlo hypothesis testing to generate P-values for these regions. The 'rsatscan' package provides functions for writing R data frames in 'SaTScan'-readable formats, for setting 'SaTScan' parameters, for running 'SaTScan' in the OS, and for reading the files that 'SaTScan' creates.
Maintained by Scott Hostovich. Last updated 9 months ago.
4.1 match 8 stars 5.45 score 35 scripts
nononoexe
rrstools:Tools for Analyzing RoboCupRescue Simulation Data
Provides functions for analyzing RoboCupRescue Simulation data.
Maintained by Keisuke ANDO. Last updated 3 months ago.
geomaprcrsrobocuprpackagesrrsvisualization
11.0 match 2.00 score 2 scriptsropensci
rgbif:Interface to the Global Biodiversity Information Facility API
A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/developer/summary>). GBIF is a database of species occurrence records from sources all over the globe. rgbif includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, getting counts of occurrence records, and using the GBIF tile map service to make rasters summarizing huge amounts of data.
Maintained by John Waller. Last updated 2 days ago.
gbifspecimensapiweb-servicesoccurrencesspeciestaxonomybiodiversitydatalifewatchoscibiospocc
1.7 match 161 stars 13.26 score 2.1k scripts 20 dependents
dgrtwo
fuzzyjoin:Join Tables Together on Inexact Matching
Join tables together based not on whether columns match exactly, but whether they are similar by some comparison. Implementations include string distance and regular expression matching.
Maintained by David Robinson. Last updated 5 years ago.
1.7 match 678 stars 12.92 score 1.5k scripts 20 dependents
jeffreyevans
spatialEco:Spatial Analysis and Modelling Utilities
Utilities to support spatial data manipulation, query, sampling and modelling in ecological applications. Functions include models for species population density, spatial smoothing, multivariate separability, point process model for creating pseudo- absences and sub-sampling, Quadrant-based sampling and analysis, auto-logistic modeling, sampling models, cluster optimization, statistical exploratory tools and raster-based metrics.
Maintained by Jeffrey S. Evans. Last updated 11 days ago.
biodiversityconservationecologyr-spatialrasterspatialvector
2.3 match 110 stars 9.55 score 736 scripts 2 dependentsbioc
annotate:Annotation for microarrays
Using R enviroments for annotation.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
1.8 match 11.41 score 812 scripts 243 dependentsropensci
spatsoc:Group Animal Relocation Data by Spatial and Temporal Relationship
Detects spatial and temporal groups in GPS relocations (Robitaille et al. (2019) <doi:10.1111/2041-210X.13215>). It can be used to convert GPS relocations to gambit-of-the-group format to build proximity-based social networks In addition, the randomizations function provides data-stream randomization methods suitable for GPS data.
Maintained by Alec L. Robitaille. Last updated 1 months ago.
2.0 match 24 stars 9.97 score 145 scripts 3 dependentsbioc
CEMiTool:Co-expression Modules identification Tool
The CEMiTool package unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.
Maintained by Helder Nakaya. Last updated 5 months ago.
geneexpressiontranscriptomicsgraphandnetworkmrnamicroarrayrnaseqnetworknetworkenrichmentpathwaysimmunooncology
3.4 match 5.76 score 38 scripts
opengeos
whitebox:'WhiteboxTools' R Frontend
An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. Suggested citation: Lindsay (2016) <doi:10.1016/j.cageo.2016.07.003>.
Maintained by Andrew Brown. Last updated 5 months ago.
geomorphometrygeoprocessinggeospatialgishydrologyremote-sensingrstudio
1.9 match 173 stars 9.65 score 203 scripts 2 dependentsropengov
geofi:Access Finnish Geospatial Data
Designed to simplify geospatial data access from the Statistics Finland Web Feature Service API <https://geo.stat.fi/geoserver/index.html>, the geofi package offers researchers and analysts a set of tools to obtain and harmonize administrative spatial data for a wide range of applications, from urban planning to environmental research. The package contains annually updated time series of municipality key datasets that can be used for data aggregation and language translations.
Maintained by Markus Kainu. Last updated 1 months ago.
2.2 match 20 stars 8.17 score 61 scriptsbioc
GEOsubmission:Prepares microarray data for submission to GEO
Helps to easily submit a microarray dataset and the associated sample information to GEO by preparing a single file for upload (direct deposit).
Maintained by Alexandre Kuhn. Last updated 5 months ago.
5.3 match 3.30 score 2 scripts
person-c
easybio:Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit
Provides a comprehensive toolkit for single-cell annotation with the 'CellMarker2.0' database (see Xia Li, Peng Wang, Yunpeng Zhang (2023) <doi: 10.1093/nar/gkac947>). Streamlines biological label assignment in single-cell RNA-seq data and facilitates transcriptomic analysis, including preparation of TCGA<https://portal.gdc.cancer.gov/> and GEO<https://www.ncbi.nlm.nih.gov/geo/> datasets, differential expression analysis and visualization of enrichment analysis results. Additional utility functions support various bioinformatics workflows. See Wei Cui (2024) <doi: 10.1101/2024.09.14.609619> for more details.
Maintained by Wei Cui. Last updated 12 days ago.
limmageoqueryedgerfgseabioinformaticscellmarker2gsearna-seqsingle-cell
2.6 match 10 stars 6.62 score 35 scriptsbioc
EGAD:Extending guilt by association by degree
The package implements a series of highly efficient tools to calculate functional properties of networks based on guilt by association methods.
Maintained by Sara Ballouz. Last updated 5 months ago.
softwarefunctionalgenomicssystemsbiologygenepredictionfunctionalpredictionnetworkenrichmentgraphandnetworknetwork
3.5 match 4.92 score 83 scriptsbioc
casper:Characterization of Alternative Splicing based on Paired-End Reads
Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.
Maintained by David Rossell. Last updated 4 months ago.
immunooncologygeneexpressiondifferentialexpressiontranscriptionrnaseqsequencingcpp
3.3 match 5.02 score 66 scripts
appelmar
gdalcubes:Earth Observation Data Cubes from Satellite Image Collections
Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time, applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values, exporting data cubes as 'netCDF' or 'GeoTIFF' files, plotting, and extraction from spatial and or spatiotemporal features. All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries. See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Maintained by Marius Appel. Last updated 1 years ago.
remote-sensingsatellite-imageryspatial-analysisgdalnetcdfcpp
1.9 match 124 stars 8.39 score 356 scriptsbioc
pairedGSEA:Paired DGE and DGS analysis for gene set enrichment analysis
pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes with a wrapper function for running an Over-Representation Analysis (ORA) and functionalities for plotting the results.
Maintained by Sรธren Helweg Dam. Last updated 1 months ago.
differentialexpressionalternativesplicingdifferentialsplicinggeneexpressionimmunooncologygenesetenrichmentpathwaysrnaseqsoftwaretranscription
3.5 match 2 stars 4.48 score
julienmoeys
soiltexture:Functions for Soil Texture Plot, Classification and Transformation
"The Soil Texture Wizard" is a set of R functions designed to produce texture triangles (also called texture plots, texture diagrams, texture ternary plots), classify and transform soil textures data. These functions virtually allows to plot any soil texture triangle (classification) into any triangle geometry (isosceles, right-angled triangles, etc.). This set of function is expected to be useful to people using soil textures data from different soil texture classification or different particle size systems. Many (> 15) texture triangles from all around the world are predefined in the package. A simple text based graphical user interface is provided: soiltexture_gui().
Maintained by Julien Moeys. Last updated 1 years ago.
2.0 match 28 stars 7.11 score 136 scripts 1 dependents
uribo
fgdr:Utilities for Fundamental Geo-Spatial Data
Read and Parse for Fundamental Geo-Spatial Data (FGD) which downloads XML file from providing site (<https://fgd.gsi.go.jp/download/menu.php>). The JPGIS format file provided by FGD so that it can be handled as an R spatial object such as 'sf' and 'raster', 'terra' or 'stars'. Supports the FGD version 4.1, and accepts fundamental items and digital elevation models.
Maintained by Shinya Uryu. Last updated 1 years ago.
3.5 match 11 stars 4.04 score 8 scriptsbioc
SRAdb:A compilation of metadata from NCBI SRA and tools
The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, and others. However, finding data of interest can be challenging using current tools. SRAdb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.
Maintained by Jack Zhu. Last updated 3 months ago.
infrastructuresequencingdataimport
1.8 match 2 stars 7.81 score 200 scripts
mcanouil
NACHO:NanoString Quality Control Dashboard
NanoString nCounter data are gene expression assays where there is no need for the use of enzymes or amplification protocols and work with fluorescent barcodes (Geiss et al. (2018) <doi:10.1038/nbt1385>). Each barcode is assigned a messenger-RNA/micro-RNA (mRNA/miRNA) which after bonding with its target can be counted. As a result each count of a specific barcode represents the presence of its target mRNA/miRNA. 'NACHO' (NAnoString quality Control dasHbOard) is able to analyse the exported NanoString nCounter data and facilitates the user in performing a quality control. 'NACHO' does this by visualising quality control metrics, expression of control genes, principal components and sample specific size factors in an interactive web application.
Maintained by Mickaรซl Canouil. Last updated 1 years ago.
mirnamrnananostringnormalisationquality-controlshiny
2.5 match 8 stars 5.41 score 32 scripts
bioc
Cogito:Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets
Biological studies often consist of multiple conditions which are examined with different laboratory set ups like RNA-sequencing or ChIP-sequencing. To get an overview about the whole resulting data set, Cogito provides an automated, complete, reproducible and clear report about all samples and basic comparisons between all different samples. This report can be used as documentation about the data set or as starting point for further custom analysis.
Maintained by Annika Bรผrger. Last updated 5 months ago.
functionalgenomicsgeneregulationsoftwaresequencing
3.3 match 4.00 score 3 scripts
jonathanlees
GEOmap:Topographic and Geologic Mapping
Set of routines for making map projections (forward and inverse), topographic maps, perspective plots, geological maps, geological map symbols, geological databases, interactive plotting and selection of focus regions.
Maintained by Jonathan M. Lees. Last updated 8 months ago.
3.9 match 3.38 score 162 scripts 3 dependentsbioc
PCAtools:PCAtools: Everything Principal Components Analysis
Principal Component Analysis (PCA) is a very powerful technique that has wide applicability in data science, bioinformatics, and further afield. It was initially developed to analyse large volumes of data in order to tease out the differences/relationships between the logical entities being analysed. It extracts the fundamental structure of the data without the need to build any model to represent it. This 'summary' of the data is arrived at through a process of reduction that can transform the large number of variables into a lesser number that are uncorrelated (i.e. the 'principal components'), while at the same time being capable of easy interpretation on the original data. PCAtools provides functions for data exploration via PCA, and allows the user to generate publication-ready figures. PCA is performed via BiocSingular - users can also identify optimal number of principal components via different metrics, such as elbow method and Horn's parallel analysis, which has relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high dimensional mass cytometry data.
Maintained by Kevin Blighe. Last updated 5 months ago.
rnaseqatacseqgeneexpressiontranscriptionsinglecellprincipalcomponentcpp
1.2 match 343 stars 11.12 score 832 scripts 2 dependentsropengov
RPublica:ProPublica API Client
Client for accessing data journalism APIs from ProPublica <https://www.propublica.org/>.
Maintained by Thomas J. Leeper. Last updated 2 years ago.
3.0 match 23 stars 4.26 score 16 scriptsropensci
dataspice:Create Lightweight Schema.org Descriptions of Data
The goal of 'dataspice' is to make it easier for researchers to create basic, lightweight, and concise metadata files for their datasets. These basic files can then be used to make useful information available during analysis, create a helpful dataset "README" webpage, and produce more complex metadata formats to aid dataset discovery. Metadata fields are based on the 'Schema.org' and 'Ecological Metadata Language' standards.
Maintained by Bryce Mecum. Last updated 4 years ago.
datadatasetmetadataschema-orgunconfunconf18
1.7 match 162 stars 7.45 score 25 scripts
selesnow
rgoogleads:Loading Data from 'Google Ads API'
Interface for loading data from 'Google Ads API', see <https://developers.google.com/google-ads/api/docs/start>. Package provide function for authorization and loading reports.
Maintained by Alexey Seleznev. Last updated 2 months ago.
1.9 match 14 stars 6.40 score 15 scripts 1 dependents
great-northern-diver
loon.data:Data Used to Illustrate 'Loon' Functionality
Data used as examples in the 'loon' package.
Maintained by R. Wayne Oldford. Last updated 4 years ago.
3.6 match 1 stars 3.32 score 14 scripts 1 dependents
asa12138
pctax:Professional Comprehensive Omics Data Analysis
Provides a comprehensive suite of tools for analyzing omics data. It includes functionalities for alpha diversity analysis, beta diversity analysis, differential abundance analysis, community assembly analysis, visualization of phylogenetic tree, and functional enrichment analysis. With a progressive approach, the package offers a range of analysis methods to explore and understand the complex communities. It is designed to support researchers and practitioners in conducting in-depth and professional omics data analysis.
Maintained by Chen Peng. Last updated 4 months ago.
microbiomesoftwarevisualizationomics
2.0 match 14 stars 5.89 score 14 scripts
lgnbhl
BFS:Get Data from the Swiss Federal Statistical Office
Search and download data from the Swiss Federal Statistical Office (BFS) APIs <https://www.bfs.admin.ch/>.
Maintained by Felix Luginbuhl. Last updated 3 months ago.
1.8 match 18 stars 6.55 score 17 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
3.4 match 3.30 score 3 scripts
tinnlab
RCPA:Consensus Pathway Analysis
Provides a set of functions to perform pathway analysis and meta-analysis from multiple gene expression datasets, as well as visualization of the results. This package wraps functionality from the following packages: Ritchie et al. (2015) <doi:10.1093/nar/gkv007>, Love et al. (2014) <doi:10.1186/s13059-014-0550-8>, Robinson et al. (2010) <doi:10.1093/bioinformatics/btp616>, Korotkevich et al. (2016) <arxiv:10.1101/060012>, Efron et al. (2015) <https://CRAN.R-project.org/package=GSA>, and Gu et al. (2012) <https://CRAN.R-project.org/package=CePa>.
Maintained by Ha Nguyen. Last updated 4 months ago.
biobasedeseq2geoqueryedgerlimmarcyjsfgseabrowservizsummarizedexperimentannotationdbirontotools
2.0 match 1 stars 5.50 score 70 scripts
dieghernan
rasterpic:Convert Digital Images into 'SpatRaster' Objects
Generate 'SpatRaster' objects, as defined by the 'terra' package, from digital images, using a specified spatial object as a geographical reference.
Maintained by Diego Hernangรณmez. Last updated 3 days ago.
jpegjpgmapspngrastersfterratiftiff
1.8 match 12 stars 6.10 score 14 scripts
claudiofronterre
RiskMap:Geo-Statistical Modeling of Spatially Referenced Data
Provides functions for geo-statistical analysis of both continuous and count data using maximum likelihood methods. The models implemented in the package use stationary Gaussian processes with Matern correlation function to carry out spatial prediction in a geographical area of interest. The underpinning theory of the methods implemented in the package are found in Diggle and Giorgi (2019, ISBN: 978-1-138-06102-7).
Maintained by Emanuele Giorgi. Last updated 6 months ago.
3.4 match 3.18 score 5 scripts
richardli
surveyPrev:Mapping the Prevalence of Binary Indicators using Survey Data in Small Areas
Provides a pipeline to perform small area estimation and prevalence mapping of binary indicators using health and demographic survey data, described in Fuglstad et al. (2022) <doi:10.48550/arXiv.2110.09576> and Wakefield et al. (2020) <doi:10.1111/insr.12400>.
Maintained by Qianyu Dong. Last updated 3 days ago.
1.9 match 1 stars 5.76 score 11 scriptsropensci
mregions2:Access Data from Marineregions.org: Gazetteer & Data Products
Explore and retrieve marine geospatial data from the Marine Regions Gazetteer <https://marineregions.org/gazetteer.php?p=webservices> and the Marine Regions Data Products <https://marineregions.org/webservices.php>.
Maintained by Salvador Jesรบs Fernรกndez Bejarano. Last updated 18 hours ago.
1.8 match 9 stars 5.97 score 40 scriptsbioc
KnowSeq:KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
KnowSeq proposes a novel methodology that comprises the most relevant steps in the Transcriptomic gene expression analysis. KnowSeq expects to serve as an integrative tool that allows to process and extract relevant biomarkers, as well as to assess them through a Machine Learning approaches. Finally, the last objective of KnowSeq is the biological knowledge extraction from the biomarkers (Gene Ontology enrichment, Pathway listing and Visualization and Evidences related to the addressed disease). Although the package allows analyzing all the data manually, the main strenght of KnowSeq is the possibilty of carrying out an automatic and intelligent HTML report that collect all the involved steps in one document. It is important to highligh that the pipeline is totally modular and flexible, hence it can be started from whichever of the different steps. KnowSeq expects to serve as a novel tool to help to the experts in the field to acquire robust knowledge and conclusions for the data and diseases to study.
Maintained by Daniel Castillo-Secilla. Last updated 5 months ago.
geneexpressiondifferentialexpressiongenesetenrichmentdataimportclassificationfeatureextractionsequencingrnaseqbatcheffectnormalizationpreprocessingqualitycontrolgeneticstranscriptomicsmicroarrayalignmentpathwayssystemsbiologygoimmunooncology
2.9 match 3.30 score 5 scriptsbioc
bigmelon:Illumina methylation array analysis for large experiments
Methods for working with Illumina arrays using gdsfmt.
Maintained by Leonard C. Schalkwyk. Last updated 5 months ago.
dnamethylationmicroarraytwochannelpreprocessingqualitycontrolmethylationarraydataimportcpgisland
1.8 match 5.47 score 21 scripts
gbradburd
BEDASSLE:Quantifies Effects of Geo/Eco Distance on Genetic Differentiation
Provides functions that allow users to quantify the relative contributions of geographic and ecological distances to empirical patterns of genetic differentiation on a landscape. Specifically, we use a custom Markov chain Monte Carlo (MCMC) algorithm, which is used to estimate the parameters of the inference model, as well as functions for performing MCMC diagnosis and assessing model adequacy.
Maintained by Gideon Bradburd. Last updated 1 years ago.
2.9 match 2 stars 3.26 score 30 scripts 1 dependents
usaid-oha-si
gisr:Geospatial Analytics Utility functions
R Spatial functions for HIV/AIDS related Geospatial Analytics.
Maintained by Baboyma Kagniniwa. Last updated 1 years ago.
1.8 match 2 stars 5.29 score 328 scriptsbioc
SurfR:Surface Protein Prediction and Identification
Identify Surface Protein coding genes from a list of candidates. Systematically download data from GEO and TCGA or use your own data. Perform DGE on bulk RNAseq data. Perform Meta-analysis. Descriptive enrichment analysis and plots.
Maintained by Aurora Maurizio. Last updated 3 months ago.
softwaresequencingrnaseqgeneexpressiontranscriptiondifferentialexpressionprincipalcomponentgenesetenrichmentpathwaysbatcheffectfunctionalgenomicsvisualizationdataimportfunctionalpredictiongenepredictiongodgeenrichment-analysismetaanalysisplotsproteinspublic-datasurfacesurfaceome
1.7 match 3 stars 5.38 score 3 scripts
stevenmmortimer
rdfp:An Implementation of the 'DoubleClick for Publishers' API
Functions to interact with the 'Google DoubleClick for Publishers (DFP)' API <https://developers.google.com/ad-manager/api/start> (recently renamed to 'Google Ad Manager'). This package is automatically compiled from the API WSDL (Web Service Description Language) files to dictate how the API is structured. Theoretically, all API actions are possible using this package; however, care must be taken to format the inputs correctly and parse the outputs correctly. Please see the 'Google Ad Manager' API reference <https://developers.google.com/ad-manager/api/rel_notes> and this package's website <https://stevenmmortimer.github.io/rdfp/> for more information, documentation, and examples.
Maintained by Steven M. Mortimer. Last updated 6 years ago.
api-clientapi-wrapperdfpdfp-apidoubleclickdoubleclick-for-publishersgoogle-dfp
1.3 match 16 stars 6.93 score 214 scripts
r-forge
TopKLists:Inference, Aggregation and Visualization for Top-K Ranked Lists
For multiple ranked input lists (full or partial) representing the same set of N objects, the package TopKLists offers (1) statistical inference on the lengths of informative top-k lists, (2) stochastic aggregation of full or partial lists, and (3) graphical tools for the statistical exploration of input lists, and for the visualization of aggregation results.
Maintained by Michael G. Schimek. Last updated 9 years ago.
2.3 match 4.05 score 37 scripts 1 dependentsropensci
tic:Tasks Integrating Continuously: CI-Agnostic Workflow Definitions
Provides a way to describe common build and deployment workflows for R-based projects: packages, websites (e.g. blogdown, pkgdown), or data processing (e.g. research compendia). The recipe is described independent of the continuous integration tool used for processing the workflow (e.g. 'GitHub Actions' or 'Circle CI'). This package has been peer-reviewed by rOpenSci (v0.3.0.9004).
Maintained by Eli Miller. Last updated 1 months ago.
appveyorcontinuous-integrationdeploymentgithubactionstravis-ci
1.2 match 155 stars 7.57 score 16 scripts
hypertidy
affinity:Raster Georeferencing, Grid Affine Transforms, Cell Abstraction
Tools for raster georeferencing, grid affine transforms, and general raster logic. These functions provide converters between raster specifications, world vector, geotransform, 'RasterIO' window, and 'RasterIO window' in 'sf' package list format. There are functions to offset a matrix by padding any of four corners (useful for vectorizing neighbourhood operations), and helper functions to harvesting user clicks on a graphics device to use for simple georeferencing of images. Methods used are available from <https://en.wikipedia.org/wiki/World_file> and <https://gdal.org/user/raster_data_model.html>.
Maintained by Michael D. Sumner. Last updated 4 years ago.
1.9 match 14 stars 4.85 score 7 scripts
crazycapivara
owmr:OpenWeatherMap API Wrapper
Accesses OpenWeatherMap's (owm) <https://openweathermap.org/> API. 'owm' itself is a service providing weather data in the past, in the future and now. Furthermore, 'owm' serves weather map layers usable in frameworks like 'leaflet'. In order to access the API, you need to sign up for an API key. There are free and paid plans. Beside functions for fetching weather data from 'owm', 'owmr' supplies tools to tidy up fetched data (for fast and simple access) and to show it on leaflet maps.
Maintained by Stefan Kuethe. Last updated 5 years ago.
openweathermapweatherweather-data
1.9 match 26 stars 4.81 score 50 scriptsbioc
NTW:Predict gene network using an Ordinary Differential Equation (ODE) based method
This package predicts the gene-gene interaction network and identifies the direct transcriptional targets of the perturbation using an ODE (Ordinary Differential Equation) based method.
Maintained by Yuanhua Liu. Last updated 5 months ago.
2.3 match 3.78 score 1 scripts
tacazares
SeedMatchR:Find Matches to Canonical SiRNA Seeds in Genomic Features
On-target gene knockdown using siRNA ideally results from binding fully complementary regions in mRNA transcripts to induce cleavage. Off-target siRNA gene knockdown can occur through several modes, one being a seed-mediated mechanism mimicking miRNA gene regulation. Seed-mediated off-target effects occur when the ~8 nucleotides at the 5โ end of the guide strand, called a seed region, bind the 3โ untranslated regions of mRNA, causing reduced translation. Experiments using siRNA knockdown paired with RNA-seq can be used to detect siRNA sequences with potential off-target effects driven by the seed region. 'SeedMatchR' provides tools for exploring and detecting potential seed-mediated off-target effects of siRNA in RNA-seq experiments. 'SeedMatchR' is designed to extend current differential expression analysis tools, such as 'DESeq2', by annotating results with predicted seed matches. Using publicly available data, we demonstrate the ability of 'SeedMatchR' to detect cumulative changes in differential gene expression attributed to siRNA seed regions.
Maintained by Tareian Cazares. Last updated 1 years ago.
deseq2-analysismirnarna-seqsirnatranscriptomics
1.8 match 7 stars 4.54 score 7 scriptsbioc
ChIPXpress:ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
ChIPXpress takes as input predicted TF bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.
Maintained by George Wu. Last updated 5 months ago.
2.1 match 3.78 score 2 scriptsbioc
DExMA:Differential Expression Meta-Analysis
performing all the steps of gene expression meta-analysis considering the possible existence of missing genes. It provides the necessary functions to be able to perform the different methods of gene expression meta-analysis. In addition, it contains functions to apply quality controls, download GEO datasets and show graphical representations of the results.
Maintained by Juan Antonio Villatoro-Garcรญa. Last updated 5 months ago.
differentialexpressiongeneexpressionstatisticalmethodqualitycontrol
2.4 match 3.30 score 7 scripts
antoinelucas64
geotools:Geo tools
Tools
Maintained by Antoine Lucas. Last updated 17 years ago.
3.8 match 2.10 score 14 scripts 3 dependentsfumi-github
scPloidy:Infer Ploidy of Single Cells
Compute ploidy of single cells (or nuclei) based on single-cell (or single-nucleus) ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) data <https://github.com/fumi-github/scPloidy>.
Maintained by Fumihiko Takeuchi. Last updated 8 months ago.
1.5 match 3 stars 5.18 score 8 scripts
face-it-project
FjordLight:Available Light Within the Water Column and on the Seafloor of Arctic Fjords
Satellite data collected between 2003 and 2022, in conjunction with gridded bathymetric data (50-150 m resolution), are used to estimate the irradiance reaching the bottom of a series of representative EU Arctic fjords. An Earth System Science Data (ESSD) manuscript, Schlegel et al. (2024), provides a detailed explanation of the methodology.
Maintained by Robert W. Schlegel. Last updated 7 months ago.
1.7 match 4.30 score 6 scriptscran
FinancialMath:Financial Mathematics for Actuaries
Contains financial math functions and introductory derivative functions included in the Society of Actuaries and Casualty Actuarial Society 'Financial Mathematics' exam, and some topics in the 'Models for Financial Economics' exam.
Maintained by Kameron Penn. Last updated 8 years ago.
4.5 match 4 stars 1.60 score
cb4ds
DGEobj:Differential Gene Expression (DGE) Analysis Results Data Object
Provides a flexible container to manage and annotate Differential Gene Expression (DGE) analysis results (Smythe et. al (2015) <doi:10.1093/nar/gkv007>). The DGEobj has data slots for row (gene), col (samples), assays (matrix n-rows by m-samples dimensions) and metadata (not keyed to row, col, or assays). A set of accessory functions to deposit, query and retrieve subsets of a data workflow has been provided. Attributes are used to capture metadata such as species and gene model, including reproducibility information such that a 3rd party can access a DGEobj history to see how each data object was created or modified. Since the DGEobj is customizable and extensible it is not limited to RNA-seq analysis types of workflows -- it can accommodate nearly any data analysis workflow that starts from a matrix of assays (rows) by samples (columns).
Maintained by Connie Brett. Last updated 1 months ago.
1.3 match 2 stars 5.60 score 33 scripts 2 dependentshypertidy
vaster:Tools for Raster Grid Logic
Provides raster grid logic, the grid operations that don't require access to materialized data, i.e. most of them. Grids are arrays with dimension and extent, and many operations are functions of just the dimension 'nrows', 'ncols' or a combination of the dimension and the extent 'xmin', 'xmax', 'ymin', 'ymax'. Here we provide direct access to this logic without need for connection to any materialized data or formats. Grid logic includes functions that relate the cell index to row and column, or row and column to cell index, row, column or cell index to position. Cell index, and row,column posiiton exist independently of any other use of a raster grid.
Maintained by Michael Sumner. Last updated 10 months ago.
1.9 match 7 stars 3.62 score 9 scripts 2 dependents
ptarroso
phylin:Spatial Interpolation of Genetic Data
The spatial interpolation of genetic distances between samples is based on a modified kriging method that accepts a genetic distance matrix and generates a map of probability of lineage presence. This package also offers tools to generate a map of potential contact zones between groups with user-defined thresholds in the tree to account for old and recent divergence. Additionally, it has functions for IDW interpolation using genetic data and midpoints.
Maintained by Pedro Tarroso. Last updated 5 years ago.
2.3 match 2.99 score 49 scripts
cpsievert
plotlyGeoAssets:Render 'Plotly' Maps without an Internet Connection
Includes 'JavaScript' files that allow 'plotly' maps to render without an internet connection.
Maintained by Carson Sievert. Last updated 6 years ago.
1.8 match 5 stars 3.84 score 4 scripts
peterreichert
utility:Construct, Evaluate and Plot Value and Utility Functions
Construct and plot objective hierarchies and associated value and utility functions. Evaluate the values and utilities and visualize the results as colored objective hierarchies or tables. Visualize uncertainty by plotting median and quantile intervals within the nodes of objective hierarchies. Get numerical results of the evaluations in standard R data types for further processing.
Maintained by Peter Reichert. Last updated 2 years ago.
2.0 match 3.35 score 82 scripts 1 dependents
walkerke
tigris:Load Census TIGER/Line Shapefiles
Download TIGER/Line shapefiles from the United States Census Bureau (<https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html>) and load into R as 'sf' objects.
Maintained by Kyle Walker. Last updated 4 months ago.
0.5 match 331 stars 12.87 score 5.3k scripts 16 dependents
mpi-bgc-functional-biogeography
rtry:Preprocessing Plant Trait Data
Designed to support the application of plant trait data providing easy applicable functions for the basic steps of data preprocessing, e.g. data import, data exploration, selection of columns and rows, excluding trait data according to different attributes, geocoding, long- to wide-table transformation, and data export. 'rtry' was initially developed as part of the TRY R project to preprocess trait data received via the TRY database.
Maintained by Olee Hoi Ying Lam. Last updated 2 years ago.
1.1 match 24 stars 5.94 score 24 scripts
cheweichang1992
GGoutlieR:Identify Individuals with Unusual Geo-Genetic Patterns
Identify and visualize individuals with unusual association patterns of genetics and geography using the approach of Chang and Schmid (2023) <doi:10.1101/2023.04.06.535838>. It detects potential outliers that violate the isolation-by-distance assumption using the K-nearest neighbor approach. You can obtain a table of outliers with statistics and visualize unusual geo-genetic patterns on a geographical map. This is useful for landscape genomics studies to discover individuals with unusual geography and genetics associations from a large biological sample.
Maintained by Che-Wei Chang. Last updated 1 years ago.
5.2 match 1.18 score 15 scriptsbioc
ramr:Detection of Rare Aberrantly Methylated Regions in Array and NGS Data
ramr is an R package for detection of epimutations (i.e., infrequent aberrant DNA methylation events) in large data sets obtained by methylation profiling using array or high-throughput methylation sequencing. In addition, package provides functions to visualize found aberrantly methylated regions (AMRs), to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms.
Maintained by Oleksii Nikolaienko. Last updated 9 days ago.
dnamethylationdifferentialmethylationepigeneticsmethylationarraymethylseqaberrant-methylationbioconductordna-methylationepimutationmethylation-microarraysnext-generation-sequencingcppopenmp
1.3 match 4.65 score 5 scripts
ksbakar
spTimer:Spatio-Temporal Bayesian Modelling
Fits, spatially predicts and temporally forecasts large amounts of space-time data using [1] Bayesian Gaussian Process (GP) Models, [2] Bayesian Auto-Regressive (AR) Models, and [3] Bayesian Gaussian Predictive Processes (GPP) based AR Models for spatio-temporal big-n problems. Bakar and Sahu (2015) <doi:10.18637/jss.v063.i15>.
Maintained by K. Shuvo Bakar. Last updated 6 months ago.
2.0 match 2 stars 2.90 score 66 scripts 2 dependents
luomus
fgc:FinBIF geographic data conversion
Convert FinBIF data into geographic formats.
Maintained by William K. Morris. Last updated 18 days ago.
2.0 match 2.88 scoreuribo
kuniumi:Load and Handles Geo-Spatial Data on Japan's National Land
Reads datasets provided by National Land Numerical Information download service <https://nlftp.mlit.go.jp/ksj/index.html> and treats them as 'sf' of a R spatial objects.
Maintained by Shinya Uryu. Last updated 1 years ago.
2.8 match 2 stars 2.00 score 6 scriptscran
stratification:Univariate Stratification of Survey Populations
Univariate stratification of survey populations with a generalization of the Lavallee-Hidiroglou method of stratum construction. The generalized method takes into account a discrepancy between the stratification variable and the survey variable. The determination of the optimal boundaries also incorporate, if desired, an anticipated non-response, a take-all stratum for large units, a take-none stratum for small units, and a certainty stratum to ensure that some specific units are in the sample. The well known cumulative root frequency rule of Dalenius and Hodges and the geometric rule of Gunning and Horgan are also implemented.
Maintained by Louis-Paul Rivest. Last updated 3 years ago.
2.3 match 2.48 score 1 dependents
carlosyanez
auscensus:Access Australian Census Data (2006-2021)
R package to interact with Australian Census Data Packs,providing an interface to extract data across multiple censuses.
Maintained by Carlos Yรกรฑez Santibรกรฑez. Last updated 5 months ago.
1.7 match 1 stars 3.18 score 9 scriptshypertidy
guerrilla:Illustrate Various Methods of Interpolation for Irregular Data
Examples of interpolating irregular data, to illustrate the mechanics of various methods and some easy tools to run them.
Maintained by Michael Sumner. Last updated 1 years ago.
1.6 match 15 stars 3.18 score 4 scriptsbioc
ctsGE:Clustering of Time Series Gene Expression data
Methodology for supervised clustering of potentially many predictor variables, such as genes etc., in time series datasets Provides functions that help the user assigning genes to predefined set of model profiles.
Maintained by Michal Sharabi-Schwager. Last updated 5 months ago.
immunooncologygeneexpressiontranscriptiondifferentialexpressiongenesetenrichmentgeneticsbayesianclusteringtimecoursesequencingrnaseq
1.3 match 1 stars 4.00 score 3 scripts
epicentre-msf
epishiny:Tools for interactive visualisation of epidemiological data
Time, place and person analysis using the R shiny web-framework.
Maintained by Paul Cambpell. Last updated 1 years ago.
1.8 match 10 stars 2.81 score 13 scripts
ajpelu
famexploreR:Exploration of Threathened Flora field data
A shiny app that explores data from Threathened Flora. It uses customized forms to explore the data and generate several plots, tables.
Maintained by Antonio Jesรบs Pรฉrez-Luque. Last updated 4 months ago.
1.9 match 2 stars 2.60 score 2 scripts
nenuial
geographer:Geography Vizualisations
Provides function and objects to establish vizualisations for my Geography lessons.
Maintained by Pascal Burkhard. Last updated 21 days ago.
1.8 match 1 stars 2.78 scorecran
geosed:Smallest Enclosing Disc for Latitude and Longitude Points
Find the smallest circle that contains all longitude and latitude input points. From the generated center and radius, variable side polygons can be created, navigation based on bearing and distance can be applied, and more. Based on a modified version of Welzl's algorithm for smallest circle. Distance calculations are based on the haversine formula. Calculations for distance, midpoint, bearing and more are derived from <https://www.movable-type.co.uk>.
Maintained by Shant Sukljian. Last updated 6 years ago.
2.3 match 1.70 score
millstei
fdrci:Permutation-Based FDR Point and Confidence Interval Estimation
FDR functions for permutation-based estimators, including pi0 as well as FDR confidence intervals. The confidence intervals account for dependencies between tests by the incorporation of an overdispersion parameter, which is estimated from the permuted data. Also included are options for an analog parametric approach.
Maintained by Joshua Millstein. Last updated 2 years ago.
1.3 match 2.78 score 12 scripts
gschofl
reutils:Talk to the NCBI EUtils
An interface to NCBI databases such as PubMed, GenBank, or GEO powered by the Entrez Programming Utilities (EUtils). The nine EUtils provide programmatic access to the NCBI Entrez query and database system for searching and retrieving biological data.
Maintained by Gerhard Schรถfl. Last updated 4 years ago.
0.5 match 22 stars 6.95 score 135 scripts 1 dependentsbioc
phantasusLite:Loading and annotation RNA-seq counts matrices
PhantasusLite โ a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects.
Maintained by Alexey Sergushichev. Last updated 5 months ago.
geneexpressiontranscriptomicsrnaseq
0.5 match 8 stars 6.08 score 8 scripts 1 dependents
paulesantos
geoperu:Download Spatial Datasets of Peru
Provides convenient access to the official spatial datasets of Peru as 'sf' objects in R. This package includes a wide range of geospatial data covering various aspects of Peruvian geography, such as: administrative divisions (Source: INEI <https://ide.inei.gob.pe/>), protected natural areas (Source: GEO ANP - SERNANP <https://geo.sernanp.gob.pe/visorsernanp/>). All datasets are harmonized in terms of attributes, projection, and topology, ensuring consistency and ease of use for spatial analysis and visualization.
Maintained by Paul E. Santos Andrade. Last updated 4 months ago.
0.8 match 2 stars 3.95 score 5 scripts
munterfi
eRTG3D:Empirically Informed Random Trajectory Generation in 3-D
Creates realistic random trajectories in a 3-D space between two given fix points, so-called conditional empirical random walks (CERWs). The trajectory generation is based on empirical distribution functions extracted from observed trajectories (training data) and thus reflects the geometrical movement characteristics of the mover. A digital elevation model (DEM), representing the Earth's surface, and a background layer of probabilities (e.g. food sources, uplift potential, waterbodies, etc.) can be used to influence the trajectories. Unterfinger M (2018). "3-D Trajectory Simulation in Movement Ecology: Conditional Empirical Random Walk". Master's thesis, University of Zurich. <https://www.geo.uzh.ch/dam/jcr:6194e41e-055c-4635-9807-53c5a54a3be7/MasterThesis_Unterfinger_2018.pdf>. Technitis G, Weibel R, Kranstauber B, Safi K (2016). "An algorithm for empirically informed random trajectory generation between two endpoints". GIScience 2016: Ninth International Conference on Geographic Information Science, 9, online. <doi:10.5167/uzh-130652>.
Maintained by Merlin Unterfinger. Last updated 3 years ago.
3dbirdsconditional-empirical-random-walkgliding-and-soaringmachine-learningmovement-ecologyrandom-trajectory-generatorrandom-walksimulationtrajectory-generation
0.5 match 6 stars 5.71 score 19 scripts
atsyplenkov
centerline:Extract Centerline from Closed Polygons
Generates skeletons of closed 2D polygons using Voronoi diagrams. It provides methods for 'sf', 'terra', and 'geos' objects to compute polygon centerlines based on the generated skeletons. Voronoi, G. (1908) <doi:10.1515/crll.1908.134.198>.
Maintained by Anatoly Tsyplenkov. Last updated 2 months ago.
0.5 match 36 stars 5.30 score 6 scripts
jsta
ipdw:Spatial Interpolation by Inverse Path Distance Weighting
Functions are provided to interpolate geo-referenced point data via Inverse Path Distance Weighting. Useful for coastal marine applications where barriers in the landscape preclude interpolation with Euclidean distances.
Maintained by Jemma Stachelek. Last updated 2 years ago.
estuaryinterpolationpath-distances
0.5 match 13 stars 5.16 score 22 scripts
julia-dyck
EgoCor:Simple Presentation of Estimated Exponential Semi-Variograms
User friendly interface based on the R package 'gstat' to fit exponential parametric models to empirical semi-variograms in order to model the spatial correlation structure of health data. Geo-located health outcomes of survey participants may be used to model spatial effects on health in an ego-centred approach. The package contains a range of functions to help explore the spatial structure of the data as well as visualize the fit of exponential models for various metaparameter combinations with respect to the number of lag intervals and maximal distance. Furthermore, the outcome of interest can be adjusted for covariates by fitting a linear regression in a preliminary step before the semi-variogram fitting process.
Maintained by Julia Dyck. Last updated 25 days ago.
0.5 match 2 stars 5.08 score 6 scripts
iwrenner
ppmlasso:Point Process Models with LASSO-Type Penalties
Toolkit for fitting point process models with sequences of LASSO penalties ("regularisation paths"), as described in Renner, I.W. and Warton, D.I. (2013) <doi:10.1111/j.1541-0420.2012.01824.x>. Regularisation paths of Poisson point process models or area-interaction models can be fitted with LASSO, adaptive LASSO or elastic net penalties. A number of criteria are available to judge the bias-variance tradeoff.
Maintained by Ian Renner. Last updated 1 years ago.
1.7 match 2 stars 1.45 score 14 scripts
kdonnay
meltt:Matching Event Data by Location, Time and Type
Framework for merging and disambiguating event data based on spatiotemporal co-occurrence and secondary event characteristics. It can account for intrinsic "fuzziness" in the coding of events, varying event taxonomies and different geo-precision codes.
Maintained by Karsten Donnay. Last updated 8 months ago.
0.5 match 24 stars 4.64 score 12 scripts
nunzioknerr
pannotator:Visualisation and Annotation of 360 Degree Imagery
Provides a customisable R 'shiny' app for immersively visualising, mapping and annotating panospheric (360 degree) imagery. The flexible interface allows annotation of any geocoded images using up to 4 user specified dropdown menus. The app uses 'leaflet' to render maps that display the geo-locations of images and panellum <https://pannellum.org/>, a lightweight panorama viewer for the web, to render images in virtual 360 degree viewing mode. Key functions include the ability to draw on & export parts of 360 images for downstream applications. Users can also draw polygons and points on map imagery related to the panoramic images and export them for further analysis. Downstream applications include using annotations to train Artificial Intelligence/Machine Learning (AI/ML) models and geospatial modelling and analysis of camera based survey data.
Maintained by Nunzio Knerr. Last updated 4 months ago.
0.5 match 2 stars 4.70 score 8 scriptshypertidy
sfdct:Constrained Triangulation for Simple Features
Build a constrained high quality Delaunay triangulation from simple features objects, applying constraints based on input line segments, and triangle properties including maximum area, minimum internal angle. The triangulation code in 'RTriangle' uses the method of Cheng, Dey and Shewchuk (2012, ISBN:9781584887300). For a low-dependency alternative with low-quality path-based constrained triangulation see <https://CRAN.R-project.org/package=decido> and for high-quality configurable triangulation see <https://github.com/hypertidy/anglr>. Also consider comparison with the 'GEOS' lib which since version 3.10.0 includes a low quality polygon triangulation method that starts with ear clipping and refines to Delaunay.
Maintained by Michael D. Sumner. Last updated 1 years ago.
0.5 match 3 stars 4.67 score 31 scriptsbioc
EpiMix:EpiMix: an integrative tool for the population-level analysis of DNA methylation
EpiMix is a comprehensive tool for the integrative analysis of high-throughput DNA methylation data and gene expression data. EpiMix enables automated data downloading (from TCGA or GEO), preprocessing, methylation modeling, interactive visualization and functional annotation.To identify hypo- or hypermethylated CpG sites across physiological or pathological conditions, EpiMix uses a beta mixture modeling to identify the methylation states of each CpG probe and compares the methylation of the experimental group to the control group.The output from EpiMix is the functional DNA methylation that is predictive of gene expression. EpiMix incorporates specialized algorithms to identify functional DNA methylation at various genetic elements, including proximal cis-regulatory elements of protein-coding genes, distal enhancers, and genes encoding microRNAs and lncRNAs.
Maintained by Yuanning Zheng. Last updated 5 months ago.
softwareepigeneticspreprocessingdnamethylationgeneexpressiondifferentialmethylation
0.5 match 1 stars 4.48 score 7 scripts 1 dependents
jacobpstein
pii:Search Data Frames for Personally Identifiable Information
Check a data frame for personal information, including names, location, disability status, and geo-coordinates.
Maintained by Jacob Patterson-Stein. Last updated 2 months ago.
0.5 match 7 stars 4.02 score 4 scripts
christopherkenny
baf:Block Assignment Files
Download and read US Census Bureau data relationship files. Provides support for cleaning and using block assignment files since 2010, as described in <https://www.census.gov/geographies/reference-files/time-series/geo/block-assignment-files.html>. Also includes support for working with block equivalency files, used for years outside of decennial census years.
Maintained by Christopher T. Kenny. Last updated 7 months ago.
0.5 match 4.08 score 4 scripts 2 dependents
qingzhaoyu
mma:Multiple Mediation Analysis
Used for general multiple mediation analysis. The analysis method is described in Yu and Li (2022) (ISBN: 9780367365479) "Statistical Methods for Mediation, Confounding and Moderation Analysis Using R and SAS", published by Chapman and Hall/CRC; and Yu et al.(2017) <DOI:10.1016/j.sste.2017.02.001> "Exploring racial disparity in obesity: a mediation analysis considering geo-coded environmental factors", published on Spatial and Spatio-temporal Epidemiology, 21, 13-23.
Maintained by Qingzhao Yu. Last updated 2 years ago.
0.5 match 1 stars 3.96 score 61 scripts 1 dependents
wiiison
onmaRg:Import Public Health Ontario's Ontario Marginalization Index
The Ontario Marginalization Index is a socioeconomic model that is built on Statistics Canada census data. The model consists of four dimensions: In 2021, these dimensions were updated to "Material Resources" (previously called "Material Deprivation"), "Households and Dwellings" (previously called "Residential Instability"), "Age and Labour Force" (previously called "Dependency"), and "Racialized and Newcomer Populations" (previously called "Ethnic Concentration"). This update reflects a movement away from deficit-based language. 2021 data will load with these new dimension names, wheras 2011 and 2016 data will load with the historical dimension names. Each of these dimensions are imported for a variety of geographic levels (DA, CD, etc.) for the 2021, 2011 and 2016 administrations of the census. These data sets contribute to community analysis of equity with respect to Ontario's Anti-Racism Act. The Ontario Marginalization Index data is retrieved from the Public Health Ontario website: <https://www.publichealthontario.ca/en/data-and-analysis/health-equity/ontario-marginalization-index>. The shapefile data is retrieved from the Statistics Canada website: <https://www12.statcan.gc.ca/census-recensement/2011/geo/bound-limit/bound-limit-eng.cfm>.
Maintained by William Conley. Last updated 5 months ago.
healthonmargsocioeconomic-indicators
0.5 match 3.70 score 7 scripts
bioc
DrugVsDisease:Comparison of disease and drug profiles using Gene set Enrichment Analysis
This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express or GEO, or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma. Enrichment scores (Subramanian et al. PNAS 2005) are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Network visualisation of significant scores are output in Cytoscape format.
Maintained by j. Saez-Rodriguez. Last updated 5 months ago.
microarraygeneexpressionclustering
0.5 match 3.30 score 8 scripts
covidr
sfo:San Francisco International Airport Monthly Air Passengers
Provides monthly statistics on the number of monthly air passengers at SFO airport such as operating airline, terminal, geo, etc. Data source: San Francisco data portal (DataSF) <https://data.sfgov.org/Transportation/Air-Traffic-Passenger-Statistics/rkru-6vcg>.
Maintained by Rami Krispin. Last updated 2 years ago.
0.5 match 3.04 score 11 scripts
cran
GPL2025:Convert Chip ID of the GPL2015 into GeneBank Accession and ENTREZID
Convert the chip ID of GPL2025 <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL2025> to GeneBank Accession and ENTREZID <http://www.ncbi.nlm.nih.gov/gene>.
Maintained by Xiang Li. Last updated 5 years ago.
0.5 match 1.00 score