Showing 33 of total 33 results (show query)
edzer
sp:Classes and Methods for Spatial Data
Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc. From this version, 'rgdal', 'maptools', and 'rgeos' are no longer used at all, see <https://r-spatial.org/r/2023/05/15/evolution4.html> for details.
Maintained by Edzer Pebesma. Last updated 2 months ago.
127 stars 18.63 score 35k scripts 1.3k dependents
bioc
GenomicRanges:Representation and manipulation of genomic intervals
The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.
Maintained by Hervé Pagès. Last updated 4 months ago.
geneticsinfrastructuredatarepresentationsequencingannotationgenomeannotationcoveragebioconductor-packagecore-package
44 stars 17.68 score 13k scripts 1.3k 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 6 hours ago.
geospatialrasterspatialvectoronetbbprojgdalgeoscpp
560 stars 17.65 score 17k scripts 856 dependentsbioc
S4Vectors:Foundation of vector-like and list-like containers in Bioconductor
The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).
Maintained by Hervé Pagès. Last updated 2 months ago.
infrastructuredatarepresentationbioconductor-packagecore-package
18 stars 16.05 score 1.0k scripts 1.9k dependentsbioc
DelayedArray:A unified framework for working transparently with on-disk and in-memory array-like datasets
Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, ordinary arrays and, data frames.
Maintained by Hervé Pagès. Last updated 1 months ago.
infrastructuredatarepresentationannotationgenomeannotationbioconductor-packagecore-packageu24ca289073
27 stars 15.59 score 538 scripts 1.2k dependentsbioc
xcms:LC-MS and GC-MS Data Analysis
Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.
Maintained by Steffen Neumann. Last updated 15 days ago.
immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detectioncpp
196 stars 14.31 score 984 scripts 11 dependentsbioc
Gviz:Plotting data and annotation information along genomic coordinates
Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.
Maintained by Robert Ivanek. Last updated 5 months ago.
visualizationmicroarraysequencing
79 stars 13.05 score 1.4k scripts 46 dependentsbioc
Spectra:Spectra Infrastructure for Mass Spectrometry Data
The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.
Maintained by RforMassSpectrometry Package Maintainer. Last updated 22 days ago.
infrastructureproteomicsmassspectrometrymetabolomicsbioconductorhacktoberfestmass-spectrometry
41 stars 13.01 score 254 scripts 35 dependentsbioc
MSnbase:Base Functions and Classes for Mass Spectrometry and Proteomics
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
Maintained by Laurent Gatto. Last updated 15 days ago.
immunooncologyinfrastructureproteomicsmassspectrometryqualitycontroldataimportbioconductorbioinformaticsmass-spectrometryproteomics-datavisualisationcpp
131 stars 12.76 score 772 scripts 36 dependentsbioc
rtracklayer:R interface to genome annotation files and the UCSC genome browser
Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.
Maintained by Michael Lawrence. Last updated 4 days ago.
annotationvisualizationdataimportzlibopensslcurl
12.66 score 6.7k scripts 480 dependents
ncss-tech
aqp:Algorithms for Quantitative Pedology
The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.
Maintained by Dylan Beaudette. Last updated 1 months ago.
digital-soil-mappingncss-technrcspedologypedometricssoilsoil-surveyusda
55 stars 11.90 score 1.2k scripts 2 dependentsbioc
MAST:Model-based Analysis of Single Cell Transcriptomics
Methods and models for handling zero-inflated single cell assay data.
Maintained by Andrew McDavid. Last updated 5 months ago.
geneexpressiondifferentialexpressiongenesetenrichmentrnaseqtranscriptomicssinglecell
232 stars 11.28 score 1.8k scripts 5 dependentsbioc
flowCore:flowCore: Basic structures for flow cytometry data
Provides S4 data structures and basic functions to deal with flow cytometry data.
Maintained by Mike Jiang. Last updated 5 months ago.
immunooncologyinfrastructureflowcytometrycellbasedassayscpp
10.17 score 1.7k scripts 59 dependentsedzer
intervals:Tools for Working with Points and Intervals
Tools for working with and comparing sets of points and intervals.
Maintained by Edzer Pebesma. Last updated 7 months ago.
11 stars 9.50 score 122 scripts 98 dependents
flr
FLCore:Core Package of FLR, Fisheries Modelling in R
Core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at <http://flr-project.org/>.
Maintained by Iago Mosqueira. Last updated 9 days ago.
fisheriesflrfisheries-modelling
16 stars 8.78 score 956 scripts 23 dependents
bart1
move:Visualizing and Analyzing Animal Track Data
Contains functions to access movement data stored in 'movebank.org' as well as tools to visualize and statistically analyze animal movement data, among others functions to calculate dynamic Brownian Bridge Movement Models. Move helps addressing movement ecology questions.
Maintained by Bart Kranstauber. Last updated 4 months ago.
8.76 score 690 scripts 3 dependents
r-hyperspec
hyperSpec:Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)
Comfortable ways to work with hyperspectral data sets, i.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with each of the spectra. The spectra can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS, etc. More generally, any data that is recorded over a discretized variable, e.g. absorbance = f(wavelength), stored as a vector of absorbance values for discrete wavelengths is suitable.
Maintained by Claudia Beleites. Last updated 10 months ago.
data-wranglinghyperspectralimaginginfrarednmrramanspectroscopyuv-visxrf
16 stars 8.10 score 233 scripts 2 dependents
polmine
polmineR:Verbs and Nouns for Corpus Analysis
Package for corpus analysis using the Corpus Workbench ('CWB', <https://cwb.sourceforge.io>) as an efficient back end for indexing and querying large corpora. The package offers functionality to flexibly create subcorpora and to carry out basic statistical operations (count, co-occurrences etc.). The original full text of documents can be reconstructed and inspected at any time. Beyond that, the package is intended to serve as an interface to packages implementing advanced statistical procedures. Respective data structures (document-term matrices, term-co-occurrence matrices etc.) can be created based on the indexed corpora.
Maintained by Andreas Blaette. Last updated 1 years ago.
49 stars 7.96 score 311 scripts
trackage
trip:Tracking Data
Access and manipulate spatial tracking data, with straightforward coercion from and to other formats. Filter for speed and create time spent maps from tracking data. There are coercion methods to convert between 'trip' and 'ltraj' from 'adehabitatLT', and between 'trip' and 'psp' and 'ppp' from 'spatstat'. Trip objects can be created from raw or grouped data frames, and from types in the 'sp', sf', 'amt', 'trackeR', 'mousetrap', and other packages, Sumner, MD (2011) <https://figshare.utas.edu.au/articles/thesis/The_tag_location_problem/23209538>.
Maintained by Michael D. Sumner. Last updated 9 months ago.
13 stars 7.72 score 137 scripts 1 dependentsbioc
ncdfFlow:ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
Provides HDF5 storage based methods and functions for manipulation of flow cytometry data.
Maintained by Mike Jiang. Last updated 3 months ago.
immunooncologyflowcytometryzlibcpp
7.56 score 96 scripts 11 dependentsbioc
flowClust:Clustering for Flow Cytometry
Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'.
Maintained by Greg Finak. Last updated 5 months ago.
immunooncologyclusteringvisualizationflowcytometry
7.31 score 83 scripts 6 dependents
mschubert
narray:Subset- And Name-Aware Array Utility Functions
Stacking arrays according to dimension names, subset-aware splitting and mapping of functions, intersecting along arbitrary dimensions, converting to and from data.frames, and many other helper functions.
Maintained by Michael Schubert. Last updated 2 months ago.
27 stars 6.91 score 10 scripts 10 dependents
pierreroudier
spectacles:Storing, Manipulating and Analysis Spectroscopy and Associated Data
Stores and eases the manipulation of spectra and associated data, with dedicated classes for spatial and soil-related data.
Maintained by Pierre Roudier. Last updated 2 years ago.
11 stars 6.17 score 45 scripts 1 dependentsbioc
easyRNASeq:Count summarization and normalization for RNA-Seq data
Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.
Maintained by Nicolas Delhomme. Last updated 5 months ago.
geneexpressionrnaseqgeneticspreprocessingimmunooncology
5.43 score 15 scripts 1 dependents
tesselle
nexus:Sourcing Archaeological Materials by Chemical Composition
Exploration and analysis of compositional data in the framework of Aitchison (1986, ISBN: 978-94-010-8324-9). This package provides tools for chemical fingerprinting and source tracking of ancient materials.
Maintained by Nicolas Frerebeau. Last updated 25 days ago.
archaeologyarchaeological-sciencearchaeometrycompositional-dataprovenance-studies
5.21 score 26 scripts 1 dependentsbioc
podkat:Position-Dependent Kernel Association Test
This package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results.
Maintained by Ulrich Bodenhofer. Last updated 5 months ago.
geneticswholegenomeannotationvariantannotationsequencingdataimportcurlbzip2xz-utilszlibcpp
5.02 score 6 scriptsbioc
flowMerge:Cluster Merging for Flow Cytometry Data
Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Note: users should have a working copy of flowClust 2.0 installed.
Maintained by Greg Finak. Last updated 5 months ago.
immunooncologyclusteringflowcytometry
4.56 score 6 scripts 1 dependentsbioc
INSPEcT:Modeling RNA synthesis, processing and degradation with RNA-seq data
INSPEcT (INference of Synthesis, Processing and dEgradation rates from Transcriptomic data) RNA-seq data in time-course experiments or steady-state conditions, with or without the support of nascent RNA data.
Maintained by Stefano de Pretis. Last updated 5 months ago.
sequencingrnaseqgeneregulationtimecoursesystemsbiology
4.38 score 9 scripts
alexwhitworth
synthACS:Synthetic Microdata and Spatial MicroSimulation Modeling for ACS Data
Provides access to curated American Community Survey (ACS) base tables via a wrapper to library(acs). Builds synthetic micro-datasets at any user-specified geographic level with ten default attributes; and, conducts spatial microsimulation modeling (SMSM) via simulated annealing. SMSM is conducted in parallel by default. Lastly, we provide functionality for data-extensibility of micro-datasets <doi:10.18637/jss.v104.i07>.
Maintained by Alex Whitworth. Last updated 2 years ago.
acsacs-datamicrosimulationspatial-data-analysiscpp
5 stars 4.29 score 78 scripts
rformassspectrometry
Chromatograms:Infrastructure for Chromatographic Mass Spectrometry Data
The Chromatograms packages defines a efficient infrastructure for storing and handling of chromatographic mass spectrometry data. It provides different implementations of *backends* to store and represent the data. Such backends can be optimized for small memory footprint or fast data access/processing. A lazy evaluation queue and chunk-wise processing capabilities ensure efficient analysis of also very large data sets.
Maintained by Philippine Louail. Last updated 1 months ago.
infrastructureproteomicsmassspectrometrymetabolomics
1 stars 4.15 score 3 scripts
nagodem
rebmix:Finite Mixture Modeling, Clustering & Classification
Random univariate and multivariate finite mixture model generation, estimation, clustering, latent class analysis and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, Gumbel, binomial, Poisson, Dirac, uniform or circular von Mises parametric families.
Maintained by Marko Nagode. Last updated 9 months ago.
1 stars 2.66 score 43 scripts
