checkMyIndex

checkMyIndex evaluates and selects compatible index combinations for multiplex high-throughput sequencing to ensure accurate sample identification and optimal data quality.

Key Features:

• Index compatibility selection: Evaluates potential index combinations to identify compatible sets for multiplex sequencing.
• Experimental-constraint customization: Applies user-defined experimental constraints including sequencing platform specifications and desired multiplexing levels.
• Error minimization and data-quality optimization: Generates index sets that aim to minimize sequencing errors and maximize data quality.
• R/Shiny computational framework: Uses R/Shiny to process input parameters and perform the evaluations of index combinations.

Scientific Applications:

• Genomics: Supports large-scale genomic studies by enabling selection of compatible indexes for multiplexed library sequencing.
• Transcriptomics: Facilitates RNA-seq experiments that require precise sample identification across multiple conditions or time points.
• Epigenetics: Assists studies of DNA methylation and histone modification by providing accurate sample differentiation in multiplex sequencing.

Methodology:

Systematic evaluation of potential index combinations against user-defined experimental constraints using R/Shiny to generate viable index sets that minimize sequencing errors and maximize data quality.