augmentedRCBD - Analysis of Augmented Randomised Complete Block Designs

Functions for analysis of data generated from experiments in augmented randomised complete block design according to Federer, W.T. (1961) <doi:10.2307/2527837>. Computes analysis of variance, adjusted means, descriptive statistics, genetic variability statistics etc. Further includes data visualization and report generation functions.

Last updated 4 months ago

augmented-blockaugmented-designaugmented-rcbd

5.94 score 7 stars 21 scripts 1.2k downloads

rmelting - R Interface to MELTING 5

R interface to the MELTING 5 program (https://www.ebi.ac.uk/biomodels/tools/melting/) to compute melting temperatures of nucleic acid duplexes along with other thermodynamic parameters.

Last updated 4 months ago

biomedicalinformaticscheminformaticsbioconductorbioinformaticsmelting-temperatureopenjdk

4.78 score 2 stars 10 scripts 181 downloads

germinationmetrics - Seed Germination Indices and Curve Fitting

Provides functions to compute various germination indices such as germinability, median germination time, mean germination time, mean germination rate, speed of germination, Timson's index, germination value, coefficient of uniformity of germination, uncertainty of germination process, synchrony of germination etc. from germination count data. Includes functions for fitting cumulative seed germination curves using four-parameter hill function and computation of associated parameters. See the vignette for more, including full list of citations for the methods implemented.

Last updated 4 months ago

curve-fittinggerminationgermination-indicesseedseed-germination-curveseed-germination-indices

4.38 score 3 stars 26 scripts 1.0k downloads

PGRdup - Discover Probable Duplicates in Plant Genetic Resources Collections

Provides functions to aid the identification of probable/possible duplicates in Plant Genetic Resources (PGR) collections using 'passport databases' comprising of information records of each constituent sample. These include methods for cleaning the data, creation of a searchable Key Word in Context (KWIC) index of keywords associated with sample records and the identification of nearly identical records with similar information by fuzzy, phonetic and semantic matching of keywords.

Last updated 1 years ago

double-metaphonedouble-metaphone-algorithmnatural-language-processingpgrplant-genetic-resourcesrecord-linkage

4.06 score 1 stars 23 scripts 340 downloads

rpcss - Constitution of Core Collections by Principal Component Scoring Strategy

Generate a Core Collection with Principal Component Scoring Strategy (PCSS) using qualitative and/or quantitative trait data according to Hamon and Noirot (1990) <https://www.documentation.ird.fr/hor/fdi:36506>, Noirot et al. (1996) <doi:10.2307/2527837> and Noirot et al. (2003) <https://www.documentation.ird.fr/hor/fdi:010031886>.

Last updated 2 days ago

3.60 score 2 scripts 17 downloads

EvaluateCore - Quality Evaluation of Core Collections

Implements various quality evaluation statistics to assess the value of plant germplasm core collections using qualitative and quantitative phenotypic trait data according to Odong et al. (2015) <doi:10.1007/s00122-012-1971-y>.

Last updated 6 months ago

core-collectionscore-evaluationgenebankgermplasmpgrplant-genetic-resources

3.50 score 1 stars 21 scripts 817 downloads