Showing 11 of total 11 results (show query)
doi-usgs
EGRET:Exploration and Graphics for RivEr Trends
Statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm: Weighted Regressions on Time, Discharge, and Season (WRTDS).
Maintained by Laura DeCicco. Last updated 4 months ago.
usgswater-qualitywater-quality-data
90 stars 10.67 score 362 scripts 1 dependents
kollerma
robustlmm:Robust Linear Mixed Effects Models
Implements the Robust Scoring Equations estimator to fit linear mixed effects models robustly. Robustness is achieved by modification of the scoring equations combined with the Design Adaptive Scale approach.
Maintained by Manuel Koller. Last updated 1 years ago.
28 stars 8.79 score 138 scripts
dusadrian
admisc:Adrian Dusa's Miscellaneous
Contains functions used across packages 'DDIwR', 'QCA' and 'venn'. Interprets and translates, factorizes and negates SOP - Sum of Products expressions, for both binary and multi-value crisp sets, and extracts information (set names, set values) from those expressions. Other functions perform various other checks if possibly numeric (even if all numbers reside in a character vector) and coerce to numeric, or check if the numbers are whole. It also offers, among many others, a highly versatile recoding routine and some more flexible alternatives to the base functions 'with()' and 'within()'. SOP simplification functions in this package use related minimization from package 'QCA', which is recommended to be installed despite not being listed in the Imports field, due to circular dependency issues.
Maintained by Adrian Dusa. Last updated 2 days ago.
2 stars 7.63 score 20 scripts 92 dependents
bioc
FELLA:Interpretation and enrichment for metabolomics data
Enrichment of metabolomics data using KEGG entries. Given a set of affected compounds, FELLA suggests affected reactions, enzymes, modules and pathways using label propagation in a knowledge model network. The resulting subnetwork can be visualised and exported.
Maintained by Sergio Picart-Armada. Last updated 5 months ago.
softwaremetabolomicsgraphandnetworkkegggopathwaysnetworknetworkenrichment
6.01 score 32 scriptsbioc
GBScleanR:Error correction tool for noisy genotyping by sequencing (GBS) data
GBScleanR is a package for quality check, filtering, and error correction of genotype data derived from next generation sequcener (NGS) based genotyping platforms. GBScleanR takes Variant Call Format (VCF) file as input. The main function of this package is `estGeno()` which estimates the true genotypes of samples from given read counts for genotype markers using a hidden Markov model with incorporating uneven observation ratio of allelic reads. This implementation gives robust genotype estimation even in noisy genotype data usually observed in Genotyping-By-Sequnencing (GBS) and similar methods, e.g. RADseq. The current implementation accepts genotype data of a diploid population at any generation of multi-parental cross, e.g. biparental F2 from inbred parents, biparental F2 from outbred parents, and 8-way recombinant inbred lines (8-way RILs) which can be refered to as MAGIC population.
Maintained by Tomoyuki Furuta. Last updated 15 days ago.
geneticvariabilitysnpgeneticshiddenmarkovmodelsequencingqualitycontrolcpp
4 stars 5.92 score 6 scripts
gitdemont
IFC:Tools for Imaging Flow Cytometry
Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®' 'Cytek®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata/>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.
Maintained by Yohann Demont. Last updated 26 days ago.
cytometrycytometry-dataflowflow-cytometryflow-cytometry-analysisflow-cytometry-dataflow-cytometry-filesifcimageimaging-flow-cytometryimaging-flow-cytometry-datamicroscopycpp
4 stars 5.34 score 12 scriptsbioc
rCGH:Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through commercial or custom aCGH arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or Affymetrix Power Tools. rCGH also supports custom arrays, provided data complies with the expected format. This package takes over all the steps required for individual genomic profiles analysis, from reading files to profiles segmentation and gene annotations. This package also provides several visualization functions (static or interactive) which facilitate individual profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.
Maintained by Frederic Commo. Last updated 5 months ago.
acghcopynumbervariationpreprocessingfeatureextraction
4 stars 5.10 score 26 scripts 1 dependentsbioc
katdetectr:Detection, Characterization and Visualization of Kataegis in Sequencing Data
Kataegis refers to the occurrence of regional hypermutation and is a phenomenon observed in a wide range of malignancies. Using changepoint detection katdetectr aims to identify putative kataegis foci from common data-formats housing genomic variants. Katdetectr has shown to be a robust package for the detection, characterization and visualization of kataegis.
Maintained by Daan Hazelaar. Last updated 5 months ago.
wholegenomesoftwaresnpsequencingclassificationvariantannotation
5 stars 5.00 score 4 scriptsbioc
codelink:Manipulation of Codelink microarray data
This package facilitates reading, preprocessing and manipulating Codelink microarray data. The raw data must be exported as text file using the Codelink software.
Maintained by Diego Diez. Last updated 5 months ago.
microarrayonechanneldataimportpreprocessing
4.20 score 5 scripts
bernhard-da
sdcTable:Methods for Statistical Disclosure Control in Tabular Data
Methods for statistical disclosure control in tabular data such as primary and secondary cell suppression as described for example in Hundepol et al. (2012) <doi:10.1002/9781118348239> are covered in this package.
Maintained by Bernhard Meindl. Last updated 22 days ago.
1 stars 3.32 score 25 scripts 2 dependents
dimitrisk
sms:Spatial Microsimulation
Produce small area population estimates by fitting census data to survey data.
Maintained by Dimitris Kavroudakis. Last updated 9 years ago.
2.37 score 29 scripts