Showing 8 of total 8 results (show query)
bioc
CINdex:Chromosome Instability Index
The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.
Maintained by Yuriy Gusev. Last updated 5 months ago.
softwarecopynumbervariationgenomicvariationacghmicroarraygeneticssequencing
19.6 match 4.08 score 2 scripts
bczernecki
thunder:Computation and Visualisation of Atmospheric Convective Parameters
Allow to compute and visualise convective parameters commonly used in the operational prediction of severe convective storms. Core algorithm is based on a highly optimized 'C++' code linked into 'R' via 'Rcpp'. Highly efficient engine allows to derive thermodynamic and kinematic parameters from large numerical datasets such as reanalyses or operational Numerical Weather Prediction models in a reasonable amount of time. Package has been developed since 2017 by research meteorologists specializing in severe thunderstorms. The most relevant methods used in the package based on the following publications Stipanuk (1973) <https://apps.dtic.mil/sti/pdfs/AD0769739.pdf>, McCann et al. (1994) <doi:10.1175/1520-0434(1994)009%3C0532:WNIFFM%3E2.0.CO;2>, Bunkers et al. (2000) <doi:10.1175/1520-0434(2000)015%3C0061:PSMUAN%3E2.0.CO;2>, Corfidi et al. (2003) <doi:10.1175/1520-0434(2003)018%3C0997:CPAMPF%3E2.0.CO;2>, Showalter (1953) <doi:10.1175/1520-0477-34.6.250>, Coffer et al. (2019) <doi:10.1175/WAF-D-19-0115.1>, Gropp and Davenport (2019) <doi:10.1175/WAF-D-17-0150.1>, Czernecki et al. (2019) <doi:10.1016/j.atmosres.2019.05.010>, Taszarek et al. (2020) <doi:10.1175/JCLI-D-20-0346.1>, Sherburn and Parker (2014) <doi:10.1175/WAF-D-13-00041.1>, Romanic et al. (2022) <doi:10.1016/j.wace.2022.100474>.
Maintained by Bartosz Czernecki. Last updated 12 months ago.
capecinconvective-parametersdownload-soundinghodographrawinsondesevere-weatherthundertornadocpp
11.0 match 45 stars 6.31 score 7 scripts
vpnagraj
twoxtwo:Work with Two-by-Two Tables
A collection of functions for data analysis with two-by-two contingency tables. The package provides tools to compute measures of effect (odds ratio, risk ratio, and risk difference), calculate impact numbers and attributable fractions, and perform hypothesis testing. Statistical analysis methods are oriented towards epidemiological investigation of relationships between exposures and outcomes.
Maintained by VP Nagraj. Last updated 3 years ago.
4.6 match 2 stars 4.68 score 12 scriptsbioc
SPIAT:Spatial Image Analysis of Tissues
SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.
Maintained by Yuzhou Feng. Last updated 2 days ago.
biomedicalinformaticscellbiologyspatialclusteringdataimportimmunooncologyqualitycontrolsinglecellsoftwarevisualization
1.3 match 22 stars 8.59 score 69 scripts
huangzhii
lmQCM:An Algorithm for Gene Co-Expression Analysis
Implementation based on Zhang, Jie & Huang, Kun (2014) <doi:10.4137/CIN.S14021> Normalized ImQCM: An Algorithm for Detecting Weak Quasi-Cliques in Weighted Graph with Applications in Gene Co-Expression Module Discovery in Cancers. Cancer informatics, 13, CIN-S14021.
Maintained by Zhi Huang. Last updated 2 years ago.
0.8 match 5 stars 4.48 score 12 scripts
cran
aiRthermo:Atmospheric Thermodynamics and Visualization
Deals with many computations related to the thermodynamics of atmospheric processes. It includes many functions designed to consider the density of air with varying degrees of water vapour in it, saturation pressures and mixing ratios, conversion of moisture indices, computation of atmospheric states of parcels subject to dry or pseudoadiabatic vertical evolutions and atmospheric instability indices that are routinely used for operational weather forecasts or meteorological diagnostics.
Maintained by Santos J. González-Rojí. Last updated 7 years ago.
2.0 match 1.48 score 1 dependentscran
BimodalIndex:The Bimodality Index
Defines the functions used to compute the bimodal index as defined by Wang et al. (2009) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2730180/>, <doi:10.4137/CIN.S2846>.
Maintained by Kevin R. Coombes. Last updated 6 years ago.
0.5 match 2.48 score 1 dependentscran
NameNeedle:Using Needleman-Wunsch to Match Sample Names
The Needleman-Wunsch global alignment algorithm can be used to find approximate matches between sample names in different data sets. See Wang et al. (2010) <doi:10.4137/CIN.S5613>.
Maintained by Kevin R. Coombes. Last updated 2 years ago.
0.5 match 1 stars 2.00 score