R-universe search: topic:ddpcr

Showing 5 of total 5 results (show query)

bioc

twoddpcr:Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules

The twoddpcr package takes Droplet Digital PCR (ddPCR) droplet amplitude data from Bio-Rad's QuantaSoft and can classify the droplets. A summary of the positive/negative droplet counts can be generated, which can then be used to estimate the number of molecules using the Poisson distribution. This is the first open source package that facilitates the automatic classification of general two channel ddPCR data. Previous work includes 'definetherain' (Jones et al., 2014) and 'ddpcRquant' (Trypsteen et al., 2015) which both handle one channel ddPCR experiments only. The 'ddpcr' package available on CRAN (Attali et al., 2016) supports automatic gating of a specific class of two channel ddPCR experiments only.

Maintained by Anthony Chiu. Last updated 5 months ago.

ddpcr software classification

10 stars 5.78 score 4 scripts

bioc

rprimer:Design Degenerate Oligos from a Multiple DNA Sequence Alignment

Functions, workflow, and a Shiny application for visualizing sequence conservation and designing degenerate primers, probes, and (RT)-(q/d)PCR assays from a multiple DNA sequence alignment. The results can be presented in data frame format and visualized as dashboard-like plots. For more information, please see the package vignette.

Maintained by Sofia Persson. Last updated 5 months ago.

alignment ddpcr coverage multiplesequencealignment sequencematching qpcr

4 stars 5.49 score 13 scripts

bioc

Polytect:An R package for digital data clustering

Polytect is an advanced computational tool designed for the analysis of multi-color digital PCR data. It provides automatic clustering and labeling of partitions into distinct groups based on clusters first identified by the flowPeaks algorithm. Polytect is particularly useful for researchers in molecular biology and bioinformatics, enabling them to gain deeper insights into their experimental results through precise partition classification and data visualization.

Maintained by Yao Chen. Last updated 3 months ago.

ddpcr clustering multichannel classification

4.74 score 4 scripts

bioc

ddPCRclust:Clustering algorithm for ddPCR data

The ddPCRclust algorithm can automatically quantify the CPDs of non-orthogonal ddPCR reactions with up to four targets. In order to determine the correct droplet count for each target, it is crucial to both identify all clusters and label them correctly based on their position. For more information on what data can be analyzed and how a template needs to be formatted, please check the vignette.

Maintained by Benedikt G. Brink. Last updated 5 months ago.

ddpcr clustering biological-data-analysis

4 stars 4.60 score 4 scripts

bioc

PoDCall:Positive Droplet Calling for DNA Methylation Droplet Digital PCR

Reads files exported from 'QX Manager or QuantaSoft' containing amplitude values from a run of ddPCR (96 well plate) and robustly sets thresholds to determine positive droplets for each channel of each individual well. Concentration and normalized concentration in addition to other metrics is then calculated for each well. Results are returned as a table, optionally written to file, as well as optional plots (scatterplot and histogram) for both channels per well written to file. The package includes a shiny application which provides an interactive and user-friendly interface to the full functionality of PoDCall.

Maintained by Hans Petter Brodal. Last updated 2 months ago.

classification epigenetics ddpcr differentialmethylation cpgisland dnamethylation

4.30 score 5 scripts