On-target gene knockdown using siRNA ideally results from binding 
    fully complementary regions in mRNA transcripts to induce cleavage. 
    Off-target siRNA gene knockdown can occur through several modes, one being 
    a seed-mediated mechanism mimicking miRNA gene regulation. Seed-mediated 
    off-target effects occur when the ~8 nucleotides at the 5’ end of the guide 
    strand, called a seed region, bind the 3’ untranslated regions of mRNA, 
    causing reduced translation. Experiments using siRNA knockdown paired with 
    RNA-seq can be used to detect siRNA sequences with potential off-target 
    effects driven by the seed region. 'SeedMatchR' provides tools for exploring 
    and detecting potential seed-mediated off-target effects of siRNA in RNA-seq 
    experiments. 'SeedMatchR' is designed to extend current differential 
    expression analysis tools, such as 'DESeq2', by annotating results with 
    predicted seed matches. Using publicly available data, we demonstrate the 
    ability of 'SeedMatchR' to detect cumulative changes in differential gene 
    expression attributed to siRNA seed regions.

Analysis of seed germination data
    using the physiological time modelling approach. Includes functions
    to fit hydrotime and thermal-time models with the traditional approaches
    of Bradford (1990) <doi:10.1104/pp.94.2.840>
    and Garcia-Huidobro (1982) <doi:10.1093/jxb/33.2.288>. 
    Allows to fit models to grouped datasets,
    i.e. datasets containing multiple species, seedlots or experiments.

Regression analysis using common models in seed temperature studies, such as the Gaussian model (Martins, JF, Barroso, AAM, & Alves, PLCA (2017) <doi:10.1590/s0100-83582017350100039>), quadratic (Nunes, AL, Sossmeier, S, Gotz, AP, & Bispo, NB (2018) <doi: 10.17265/2161-6264/2018.06.002>) and others with potential for use, such as those implemented in the 'drc' package (Ritz, C, Baty, F, Streibig, JC, & Gerhard, D (2015). <doi:10.1371/journal.pone.0146021>), in the estimation of the ideal and cardinal temperature for the occurrence of plant seed germination. The functions return graphs with the equations automatically.