Showing 24 of total 24 results (show query)
bioc
ShortRead:FASTQ input and manipulation
This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
dataimportsequencingqualitycontrolbioconductor-packagecore-packagezlibcpp
6.6 match 8 stars 12.08 score 1.8k scripts 49 dependents
bleutner
RStoolbox:Remote Sensing Data Analysis
Toolbox for remote sensing image processing and analysis such as calculating spectral indexes, principal component transformation, unsupervised and supervised classification or fractional cover analyses.
Maintained by Konstantin Mueller. Last updated 1 months ago.
ggplot2land-cover-mappingremote-sensingspectral-unmixingsupervised-classificationunsupervised-classificationopenblascpp
5.5 match 275 stars 10.10 score 1.1k scripts
martin3141
fmriqa:Functional MRI Quality Assurance Routines
Methods for performing fMRI quality assurance (QA) measurements of test objects. Heavily based on the fBIRN procedures detailed by Friedman and Glover (2006) <doi:10.1002/jmri.20583>.
Maintained by Martin Wilson. Last updated 5 years ago.
11.5 match 2 stars 4.00 score 8 scripts
himesgroup
raqs:Interface to the US EPA Air Quality System (AQS) API
Offers functions for fetching JSON data from the US EPA Air Quality System (AQS) API with options to comply with the API rate limits. See <https://aqs.epa.gov/aqsweb/documents/data_api.html> for details of the AQS API.
Maintained by Jaehyun Joo. Last updated 1 years ago.
13.7 match 3.18 score 4 scripts 1 dependentsbioc
ABarray:Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.
Automated pipline to perform gene expression analysis for Applied Biosystems Genome Survey Microarray (AB1700) data format. Functions include data preprocessing, filtering, control probe analysis, statistical analysis in one single function. A GUI interface is also provided. The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used.
Maintained by Yongming Andrew Sun. Last updated 5 months ago.
microarrayonechannelpreprocessing
7.8 match 4.20 score 3 scripts
shixiangwang
sigminer:Extract, Analyze and Visualize Mutational Signatures for Genomic Variations
Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2021) <DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Steele Christopher D., et al. (2022) <DOI:10.1038/s41586-022-04738-6>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.
Maintained by Shixiang Wang. Last updated 5 months ago.
bayesian-nmfbioinformaticscancer-researchcnvcopynumber-signaturescosmic-signaturesdbseasy-to-useindelmutational-signaturesnmfnmf-extractionsbssignature-extractionsomatic-mutationssomatic-variantsvisualizationcpp
2.2 match 150 stars 9.48 score 123 scripts 2 dependents
ropensci
UCSCXenaTools:Download and Explore Datasets from UCSC Xena Data Hubs
Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
Maintained by Shixiang Wang. Last updated 5 months ago.
api-clientbioinformaticsccledownloadericgctcgatoiltreehouseucscucsc-xena
2.2 match 106 stars 8.55 score 163 scripts 1 dependents
darwin-eu-dev
PaRe:A Way to Perform Code Review or QA on Other Packages
Reviews other packages during code review by looking at their dependencies, code style, code complexity, and how internally defined functions interact with one another.
Maintained by Maarten van Kessel. Last updated 4 months ago.
2.9 match 3 stars 5.38 score 20 scriptsropensci
rsi:Efficiently Retrieve and Process Satellite Imagery
Downloads spatial data from spatiotemporal asset catalogs ('STAC'), computes standard spectral indices from the Awesome Spectral Indices project (Montero et al. (2023) <doi:10.1038/s41597-023-02096-0>) against raster data, and glues the outputs together into predictor bricks. Methods focus on interoperability with the broader spatial ecosystem; function arguments and outputs use classes from 'sf' and 'terra', and data downloading functions support complex 'CQL2' queries using 'rstac'.
Maintained by Michael Mahoney. Last updated 2 days ago.
1.8 match 50 stars 7.21 score 38 scripts
bumbanian
assignR:Infer Geographic Origin from Isotopic Data
Routines for re-scaling isotope maps using known-origin tissue isotope data, assigning origin of unknown samples, and summarizing and assessing assignment results. Methods are adapted from Wunder (2010, in ISBN:9789048133536) and Vander Zanden, H. B. et al. (2014) <doi:10.1111/2041-210X.12229> as described in Ma, C. et al. (2020) <doi:10.1111/2041-210X.13426>.
Maintained by Gabe Bowen. Last updated 4 months ago.
3.3 match 3.48 score 30 scripts
pecanproject
PEcAn.photosynthesis:PEcAn functions used for leaf-level photosynthesis calculations
The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. The PEcAn.photosynthesis package contains functions used in the Hierarchical Bayesian calibration of the Farquhar et al 1980 model.
Maintained by Mike Dietze. Last updated 18 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsjagscpp
1.3 match 216 stars 8.84 score 19 scripts
staffanbetner
rethinking:Statistical Rethinking book package
Utilities for fitting and comparing models
Maintained by Richard McElreath. Last updated 4 months ago.
2.0 match 5.42 score 4.4k scripts
taikisan21
PAMmisc:Miscellaneous Functions for Passive Acoustic Analysis
A collection of miscellaneous functions for passive acoustics. Much of the content here is adapted to R from code written by other people. If you have any ideas of functions to add, please contact Taiki Sakai.
Maintained by Taiki Sakai. Last updated 2 days ago.
1.8 match 4 stars 5.91 score 42 scripts 2 dependents
robitalec
irg:Instantaneous Rate of Green Up
Fits a double logistic function to NDVI time series and calculates instantaneous rate of green (IRG) according to methods described in Bischoff et al. (2012) <doi:10.1086/667590>.
Maintained by Alec L. Robitaille. Last updated 4 months ago.
2.0 match 3 stars 4.98 score 32 scripts
cshs-hydrology
CSHShydRology:Canadian Hydrological Analyses
A collection of user submitted functions to aid in the analysis of hydrological data.
Maintained by Kevin Shook. Last updated 3 years ago.
1.6 match 4 stars 5.26 score 23 scriptsbioc
spiky:Spike-in calibration for cell-free MeDIP
spiky implements methods and model generation for cfMeDIP (cell-free methylated DNA immunoprecipitation) with spike-in controls. CfMeDIP is an enrichment protocol which avoids destructive conversion of scarce template, making it ideal as a "liquid biopsy," but creating certain challenges in comparing results across specimens, subjects, and experiments. The use of synthetic spike-in standard oligos allows diagnostics performed with cfMeDIP to quantitatively compare samples across subjects, experiments, and time points in both relative and absolute terms.
Maintained by Tim Triche. Last updated 5 months ago.
differentialmethylationdnamethylationnormalizationpreprocessingqualitycontrolsequencing
1.8 match 2 stars 4.90 score 3 scriptsbioc
VariantTools:Tools for Exploratory Analysis of Variant Calls
Explore, diagnose, and compare variant calls using filters.
Maintained by Michael Lawrence. Last updated 5 months ago.
geneticsgeneticvariabilitysequencing
2.0 match 4.09 score 41 scripts
europeanifcbgroup
iRfcb:Tools for Managing Imaging FlowCytobot (IFCB) Data
A comprehensive suite of tools for managing, processing, and analyzing data from the IFCB. I R FlowCytobot ('iRfcb') supports quality control, geospatial analysis, and preparation of IFCB data for publication in databases like <https://www.gbif.org>, <https://www.obis.org>, <https://emodnet.ec.europa.eu/en>, <https://shark.smhi.se/>, and <https://www.ecotaxa.org>. The package integrates with the MATLAB 'ifcb-analysis' tool, which is described in Sosik and Olson (2007) <doi:10.4319/lom.2007.5.204>, and provides features for working with raw, manually classified, and machine learning–classified image datasets. Key functionalities include image extraction, particle size distribution analysis, taxonomic data handling, and biomass concentration calculations, essential for plankton research.
Maintained by Anders Torstensson. Last updated 3 days ago.
1.3 match 1 stars 5.72 score
pharmaverse
envsetup:Support the Setup of the R Environment for Clinical Trial Programming Workflows
The purpose of this package is to support the setup the R environment. The two main features are 'autos', to automatically source files and/or directories into your environment, and 'paths' to consistently set path objects across projects for input and output. Both are implemented using a configuration file to allow easy, custom configurations that can be used for multiple or all projects.
Maintained by Nicholas Masel. Last updated 9 months ago.
1.1 match 7 stars 4.54 score 5 scripts
jaehyunjoo
LCMSQA:Liquid Chromatography/Mass Spectrometry (LC/MS) Quality Assessment
The goal of 'LCMSQA' is to make it easy to check the quality of liquid chromatograph/mass spectrometry (LC/MS) experiments using a 'shiny' application. This package provides interactive data visualizations for quality control (QC) samples, including total ion current chromatogram (TIC), base peak chromatogram (BPC), mass spectrum, extracted ion chromatogram (XIC), and feature detection results from internal standards or known metabolites.
Maintained by Jaehyun Joo. Last updated 1 years ago.
1.8 match 2.70 score 2 scripts
medhat-mahmoud
PhenoSpectra:Multispectral Data Analysis and Visualization
Provides tools for processing, analyzing, and visualizing spectral data collected from 3D laser-based scanning systems. Supports applications in agriculture, forestry, environmental monitoring, industrial quality control, and biomedical research. Enables evaluation of plant growth, productivity, resource efficiency, disease management, and pest monitoring. Includes statistical methods for extracting insights from multispectral and hyperspectral data and generating publication-ready visualizations. See Zieschank & Junker (2023) <doi:10.3389/fpls.2023.1141554> and Saric et al. (2022) <doi:10.1016/J.TPLANTS.2021.12.003> for related work.
Maintained by Medhat Mahmoud. Last updated 14 days ago.
1.7 match 2.70 scorebioc
affyContam:structured corruption of affymetrix cel file data
structured corruption of cel file data to demonstrate QA effectiveness
Maintained by V. Carey. Last updated 5 months ago.
0.6 match 3.30 score 1 scripts
cran
Rivivc:In Vitro in Vivo Correlation Linear Level "A"
It is devoted to the IVIVC linear level A with numerical deconvolution method. The latter is working for inequal and incompatible timepoints between impulse and response curves. A numerical convolution method is also available. Application domains include pharamaceutical industry QA/QC and R&D together with academic research.
Maintained by Aleksander Mendyk. Last updated 3 years ago.
0.5 match 1.00 score