#ddPCR
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cranupdates.bsky.social
New on CRAN: ddpcr (1.15.2). View at https://CRAN.R-project.org/package=ddpcr
ddpcr: Analysis and Visualization of Droplet Digital PCR in R and on the Web
An interface to explore, analyze, and visualize droplet digital PCR (ddPCR) data in R. This is the first non-proprietary software for analyzing two-channel ddPCR data. An interactive tool was also created and is available online to facilitate this analysis for anyone who is not comfortable with using R.
CRAN.R-project.org
November 8, 2025 at 9:17 PM
cranberriesfeed.bsky.social
CRAN readmissions: ddpcr freqpcr gspcr lulcc MCMC.qpcr qcQpcr rtpcr spcr #rstats
November 8, 2025 at 7:02 PM
cranberriesfeed.bsky.social
CRAN removals: autoplotly bayesAB bcfrailphdv benchr checkpoint clifro cmcR coreCollection dams ddpcr duke dyn.log dynamic fitode forestPSD freqdom.fda freqpcr funLBM gamboostMSM geneHapR #rstats
November 7, 2025 at 10:02 PM
cranupdates.bsky.social
Removed from CRAN: CopSens (0.1.0), coreCollection (0.9.5), dams (0.3.0), ddpcr (1.15.2), DiSCos (0.1.1), duke (0.0.3), dyn.log (0.4.0), dynamic (1.1.0), fitode (0.1.1), forestPSD (1.0.0), freqdom.fda (1.0.1), freqpcr (0.4.0), funLBM (2.3)
November 7, 2025 at 9:16 PM
mrc-tu.bsky.social
A new PhD student in the Willis Lab, Alexander Chalk has just had his masters/research assistant work published!

Alex and his colleagues developed a new laboratory method called CLEAR-Time ddPCR that measures exactly what happens to DNA after gene editing.

Find out more: buff.ly/wkfiI51
November 5, 2025 at 6:04 PM
docusalut.bsky.social
Nou article a #Docusalut: 🦠🏥Airborne SARS-CoV-2 Detection by ddPCR in Adequately Ventilated Hospital Corridors http://hdl.handle.net/20.500.13003/25703 @idisba.bsky.social  #PublicaSalutIB
November 4, 2025 at 9:01 AM
jmdiagn.bsky.social
A novel ddPCR assay for BRCA1 and RAD51C methylation: Advancing HRD Detection in Ovarian Cancer.

Full text: https://www.jmdjournal.org/article/S1525-1578(25)00182-5/fulltext
A novel ddPCR assay for BRCA1 and RAD51C methylation: Advancing HRD Detection in Ovarian Cancer
Homologous recombination deficiency (HRD) affects 50% of ovarian cancers (OC) and influences PARP inhibitors efficacy. While one-third of HRD tumours harbour a deleterious BRCA1/2 mutation, these mutations are not the sole cause of HRD. Promoter methylation of BRCA1 and RAD51C contributes to 19% and 2% of cases, respectively.A cohort of 224 ovarian cancer (OC) patients tested for HRD validated our droplet digital PCR (ddPCR) technique. DNA was extracted from FFPE tissue, and the Genomic Insta...
www.jmdjournal.org
October 17, 2025 at 4:12 PM
ucldiscovery.bsky.social
Open Access UCL Research: Absolute quantification of rare gene targets in limited samples using crude lysate and ddPCR discovery.ucl.ac.uk/id/eprint/10...
Absolute quantification of rare gene targets in limited samples using crude lysate and ddPCR - UCL Discovery
UCL Discovery is UCL's open access repository, showcasing and providing access to UCL research outputs from all UCL disciplines.
discovery.ucl.ac.uk
October 14, 2025 at 10:56 AM
jmdiagn.bsky.social
The October issue of @jmdiagn.bsky.social is now live online!

Full issue: https://www.jmdjournal.org/issue/S1525-1578(24)X0012-4

#hemoglobinopathy #hereditarycancer #exomesequencing #ddPCR
September 24, 2025 at 7:50 PM
marinednadude.bsky.social
A lot of eDNA work is qPCR or ddPCR based onlinelibrary.wiley.com/doi/full/10....

There’s also a lot of work trying to get at quantitative metabarcoding approaches (hard, doable-ish, active area of research) doi.org/10.1002/ecy....
Toward quantitative metabarcoding
Amplicon-sequence data from environmental DNA (eDNA) and microbiome studies provide important information for ecology, conservation, management, and health. At present, amplicon-sequencing studies—kn...
doi.org
September 23, 2025 at 9:17 PM
bioinfoadv.bsky.social
🧪 Now published in Bioinformatics Advances: "HeraNorm: An R Shiny application for identifying optimal endogenous controls for miRNA and RNA assays in qPCR and ddPCR"  

Read the full paper here: https://doi.org/10.1093/bioadv/vbaf220
September 19, 2025 at 9:02 AM
phytopathology.bsky.social
Mehdi Kamali Dashtarzhaneh et al. developed a novel LAMP assay and compared detection results with ddPCR for avocado sunblotch viroid. Both outperformed RT-LAMP, offering sensitive, reliable tools for early viroid detection and improved disease management. https://doi.org/10.1094/PHYTO-02-25-0064-R
Fig. 1. A, Distribution of avocado samples collected from Southern California avocado orchards. The Southern California map was obtained from the California State Association of Counties 2024. Green dots represent avocado sunblotch viroid (ASBVd)-infected trees and surrounding trees tested in blocks. The right box shows a testing block containing symptomatic infected trees (red) and surrounding trees (green). B, ASBVd symptoms on avocado trees. a, Sunken yellow lesions. b, Purple lesions and blotches on the avocado fruit surface. c, Leaf discoloration and distortion with reduced size. d, Narrow streaks of discoloration and indentation on the branch surface. e, Rectangular cracking of the bark on the trunk, which is referred to as “alligator bark.”
September 18, 2025 at 9:09 PM
chloefouilloux.bsky.social
If you've ever been curious about #ddPCR then my latest YouTube video is just for you! From calculating reagents to interpreting live output, we have got you covered. youtu.be/R0MlmPoF0u4
ddPCR Tutorial: From calculating reagents to reading live results!
YouTube video by Chloe Fouilloux
youtu.be
September 18, 2025 at 2:58 PM
ulikluemper.bsky.social
We argue that, in addition to quantification, assessing which and what proportion of ARGs can move via MGEs is key for predicting environmental #AMR risks. We outline tools, from ddPCR linkage to hybrid metagenomics, to make this part of routine monitoring and integrate it into QMRA.

2/3
September 16, 2025 at 12:26 PM
partridgecg.bsky.social
Is anyone in Michigan looking for an amazing lab technician with experience in sequencing library prep, ddPCR, and qPCR and a MS in public health? If so, I have the PERFECT candidate for you!!
August 29, 2025 at 1:53 PM
biorxiv-microbiol.bsky.social
ddOTs: a multiplexed quantitative ddPCR approach for resolving overlapping hepatitis B virus transcripts to decipher cccDNA-driven transcription https://www.biorxiv.org/content/10.1101/2025.08.27.672646v1
August 28, 2025 at 3:17 AM
biorxivpreprint.bsky.social
ddOTs: a multiplexed quantitative ddPCR approach for resolving overlapping hepatitis B virus transcripts to decipher cccDNA-driven transcription https://www.biorxiv.org/content/10.1101/2025.08.27.672646v1
August 28, 2025 at 3:17 AM
chasenlouie.bsky.social
We masked the pseudogenes and aligned all reads to NCF1, allowing variant calling. (Fig 2A). Using 1000G as a reference, we show that most NCF1-CGD patients carry 6 copies of the 2-base deletion (Fig 2B) and the variant frequency (AltAB) of that is in concordance with ddPCR data (fig 2C)
August 27, 2025 at 2:04 PM
helixbrief.bsky.social
Evaluating this methyl-ddPCR on an internal cohort, they found it correctly classified 90.4% of cases, correlating with prognostic markers.
August 27, 2025 at 1:29 PM
helixbrief.bsky.social
This study developed a single methylation-specific droplet digital PCR (methyl-ddPCR) test to predict IGHV mutation status in chronic lymphocytic leukemia (CLL) patients.
August 27, 2025 at 1:29 PM
l-cmurphy.bsky.social
Using flow cytometry, ddPCR, and high-resolution imaging we confirmed that plts do indeed take up DNA fragments shed by nucleated cells! In the movie below, a plt (blue) sequesters DNA (labelled in pink) from a nucleated colorectal cancer cell! 🔬6/19
August 14, 2025 at 6:35 PM
l-cmurphy.bsky.social
Using flow cytometry, ddPCR, and high-resolution imaging we confirmed that plts do indeed take up DNA fragments shed by nucleated cells! In the movie below, a plt (blue) sequesters DNA (labelled in pink) from a nucleated colorectal cancer cell! 🔬6/19
August 14, 2025 at 6:29 PM
dlingenfelter.bsky.social
Autopsies confirm SARS-CoV-2 RNA in the brain, but most damage arises from indirect effects: hypoxia, clotting, and immune overdrive—not direct viral destruction.

Glial cells, especially astrocytes, show viral tropism.
davidlingenfelter.substack.com/p/sars-cov-2...
Here’s a structured summary of the key findings from David Lingenfelter’s exhaustive review on SARS-CoV-2 in the central nervous system (CNS): ________________________________________ 🧠 Core Findings • Viral RNA Confirmed in Brain: Autopsies show SARS-CoV-2 RNA in CNS tissue, but its presence is inconsistent and often low in quantity. • Indirect Damage Dominates: Brain injury is primarily due to hypoxia, clotting, and immune overactivation—not direct viral destruction. • Astrocyte-Centric Model: The virus preferentially infects astrocytes, disrupting their support functions and triggering neuroinflammation that harms neurons indirectly. ________________________________________ 🧪 Detection Methods • PCR & ddPCR: Highly sensitive for RNA fragments but can’t confirm active infection. • In Situ Hybridization (ISH): Maps viral RNA within brain cells; antisense RNA indicates replication. • Immunohistochemistry (IHC): Detects viral proteins, suggesting recent infection. • Viral Culture: Gold standard for proving active infection, but rarely successful postmortem. ________________________________________ 🧬 Cellular & Anatomical Tropism • Astrocytes: Main targets; infection disrupts metabolic and immune regulation. • Neurons: Rarely infected directly; damage is often secondary. • Vascular Cells: Viral presence at blood-brain barrier contributes to inflammation and clotting. • Entry Mechanisms: Uses alternative receptors (NRP1, CD147, DPP4) due to low ACE2 expression in brain. ________________________________________ 🧩 Replication vs. Persistence • Replication Evidence: Viable virus and subgenomic RNA found in some early-death cases. • Persistence Model: Viral RNA/proteins linger long after acute infection, possibly driving chronic symptoms. • Timing Matters: Early deaths show replication; later deaths show residual viral debris. ________________________________________ 🧠 Neuropathological Damage • Hypoxic-Ischemic Injury: Most common; reflects systemic respiratory failu…
August 11, 2025 at 12:02 AM
jmdiagn.bsky.social
#ArticleinPress: A novel ddPCR assay for BRCA1 and RAD51C methylation: Advancing HRD Detection in Ovarian Cancer.

Full text: https://www.jmdjournal.org/article/S1525-1578(25)00182-5/fulltext
A novel ddPCR assay for BRCA1 and RAD51C methylation: Advancing HRD Detection in Ovarian Cancer
Homologous recombination deficiency (HRD) affects 50% of ovarian cancers (OC) and influences PARP inhibitors efficacy. While one-third of HRD tumours harbour a deleterious BRCA1/2 mutation, these mutations are not the sole cause of HRD. Promoter methylation of BRCA1 and RAD51C contributes to 19% and 2% of cases, respectively.A cohort of 224 ovarian cancer (OC) patients tested for HRD validated our droplet digital PCR (ddPCR) technique. DNA was extracted from FFPE tissue, and the Genomic Insta...
www.jmdjournal.org
August 8, 2025 at 5:12 PM
scienmag.bsky.social
Droplet PCR Precisely Measures FRS2 in Bladder Cancer

A groundbreaking advancement in molecular diagnostics promises to revolutionize bladder cancer analysis, offering unprecedented precision in measuring genetic alterations. Researchers have developed a droplet digital PCR (ddPCR) assay…
Droplet PCR Precisely Measures FRS2 in Bladder Cancer
A groundbreaking advancement in molecular diagnostics promises to revolutionize bladder cancer analysis, offering unprecedented precision in measuring genetic alterations. Researchers have developed a droplet digital PCR (ddPCR) assay specifically designed to quantify the fibroblast growth factor receptor substrate 2 (FRS2) gene copy number in formalin-fixed paraffin-embedded (FFPE) bladder cancer tissues. This innovative technique heralds a new era of accurate and reliable genomic profiling, potentially enhancing diagnostic and prognostic capabilities in oncology.
scienmag.com
August 4, 2025 at 5:15 AM