RDML - Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files

Imports real-time thermo cycler (qPCR) data from Real-time PCR Data Markup Language (RDML) and transforms to the appropriate formats of the 'qpcR' and 'chipPCR' packages. Contains a dendrogram visualization for the structure of RDML object and GUI for RDML editing.

Last updated 5 months ago

bioinformaticspcrqpcrrdml

7.16 score 21 stars 1 dependents 58 scripts 281 downloads

chipPCR - Toolkit of Helper Functions to Pre-Process Amplification Data

A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. Contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experimental nucleic acid amplification systems ('VideoScan HCU', capillary convective PCR (ccPCR)) and commercial systems are included. Amplification curves were generated by helicase dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used. For more information see: Roediger et al. (2015) <doi:10.1093/bioinformatics/btv205>.

Last updated 4 years ago

6.84 score 8 stars 1 dependents 97 scripts 865 downloads

MBmca - Nucleic Acid Melting Curve Analysis

Lightweight utilities for nucleic acid melting curve analysis are important in life sciences and diagnostics. This software can be used for the analysis and presentation of melting curve data from microbead-based assays (surface melting curve analysis) and reactions in solution (e.g., quantitative PCR (qPCR), real-time isothermal Amplification). Further information are described in detail in two publications in The R Journal [ <https://journal.r-project.org/archive/2013-2/roediger-bohm-schimke.pdf>; <https://journal.r-project.org/archive/2015-1/RJ-2015-1.pdf>].

Last updated 4 years ago

4.53 score 4 stars 17 scripts 278 downloads

shinyMolBio - Molecular Biology Visualization Tools for 'Shiny' Apps

Interactive visualization of 'RDML' files via 'shiny' apps. Package provides (1) PCR plate interface with ability to select individual tubes; (2) amplification/melting plots with fast hiding and highlighting individual curves; (3) 2D allelic discrimination plot.

Last updated 3 months ago

pcrqpcrrdmlshinyvisualization

4.10 score 6 stars 14 scripts 188 downloads