Tag: GAM
What is the node_id in vg giraffe output (gaf or gam)?
What is the node_id in vg giraffe output (gaf or gam)? 0 Hi, I am playing with the genome graph I built from 2 different individual whole genome sequencing data. Also, I generated 1 million simulated reads. However, while I tried to map the simulated read back to the genome…
ggplot2 – How to add a rectangle to a ggplot graph with a logged y-axis without changing the y-axis scale
I am trying to add a rectangle to a ggplot graph with a logged y-axis using annotate() or geom_rect(). The rectangle is bounded by two x-axis values (which are dates) and needs span the enitre y-axis. However, whenever I add the rectangle, it changes the scale of the y-axis. For…
You will be using RStudio to pull the data set and
You will be using RStudio to pull the data set and answer the following questions. Task 1 of 2: You will be using Boston data set to predict per capita crime rate using the other variables in this data set. 1. To begin, load in the Boston data set. The…
Quantitative Synthetic Biology for Biologics Production
Biologics accounted for more new drug approvals than did small molecules for the first time in 2022, marking a significant shift in the pharmaceutical industry (1). Large-molecule pipelines are also moving from standard monoclonal antibodies (MAbs) to more complex and difficult-to-express molecules, which intensifies pressure on the industry to meet…
Application of CRISPR/Cas9-mediated gene editing for abiotic stress management in crop plants
1 Introduction Abiotic stresses such as drought, heat, cold, salt, pesticides, metals and metalloids deteriorate agro-ecological conditions and hence, negatively impact upon agricultural production. The abiotic stress impairs with regular growth and development of plant plants, thus limiting their yield and quality of produce (Boyer, 1982; Pandey et al., 2017). Plants…
r – Combining logaritmic with non-logaritmic data
I want to show the correlation between for example loudness and streams for a spotify dataset. Therefore I want to graph the correlation. The first image is what I get using Spearman for the correlation and for the plot geom_smooth with the gam method: If i make the dataset logaritmic…
Advance on engineering of bacteriophages
Introduction Bacteriophage (phage) is a class of widespread viruses exclusively infecting bacteria, playing a key role in ecosystems.1–3 Since phages were discovered over a hundred years ago, many techniques and reagents, such as DNA polymerase, restriction endonuclease, ligase, and CRISPR/Cas system, have been developed from phages, which have together accelerated…
Recent advances in CRISPR-based genome editing technology and its applications in cardiovascular research | Military Medical Research
Doudna JA, Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014;346(6213):1258096. Article PubMed Google Scholar Doudna JA. The promise and challenge of therapeutic genome editing. Nature. 2020;578(7794):229–36. Article CAS PubMed PubMed Central Google Scholar Nambiar TS, Baudrier L, Billon P, Ciccia A. CRISPR-based genome editing…
Converting gam to gaf
Converting gam to gaf 1 I noticed it is now possible to output alignments in gaf files instead of gam, which is great! How difficult would it be to convert gam to gaf? Gaf is definitely easier to parse than using jq for the json conversion of gam, but I’d…
Speed up vg call ?
Speed up vg call ? 1 Dear all, has anyone found a good way of speeding up vg call by chunking or another method ? Current chunking seems to lead to a very modest speedup of 0-20% so maybe is not the right approach. Specifically, I have aligned with vg…
Genome editing techniques based on bacterial-artificial-chromosome in herpesvirus research
In a recent study published in the Microorganisms journal, researchers in China reviewed the uses of bacterial-artificial-chromosome (BAC)-based genome editing techniques in herpesvirus research. Review: Bacterial-Artificial-Chromosome-Based Genome Editing Methods and the Applications in Herpesvirus Research. Image Credit: Panuwach / Shutterstock Herpesviruses are significant human and animal pathogens. Exploring the role of specific…
Kenya: IPC Acute Food Insecurity and Acute Malnutrition Analysis (February – June 2023) Published on 20 February 2023 – Kenya
Attachments In the current period, February 2023, corresponding to the short rain harvest season, a slight decrease in the severity of food insecurity is observed across Kenya’s ASAL areas, which presented four counties in IPC AFI Phase 4 (Emergency) in the previous season (namely Isiolo, Turkana, Marsabit and Mandera) that…
Human mtDNA Haplogroup Classification Using a Pangenomic Reference Graph
Tool:HaploCart: Human mtDNA Haplogroup Classification Using a Pangenomic Reference Graph 0 Current mitochondrial DNA (mtDNA) haplogroup classification tools map reads to a single reference genome and perform inference based on the detected mutations to this reference. This approach biases haplogroup assignments towards the reference and prohibits accurate calculations of the…
miceforest vs scikit-learn – compare differences and reviews?
What are some alternatives? When comparing miceforest and scikit-learn you can also consider the following projects: Keras – Deep Learning for humans Prophet – Tool for producing high quality forecasts for time series data that has multiple seasonality with linear or non-linear growth. Surprise – A Python scikit for building…
Emerging role of STING signalling in CNS injury: inflammation, autophagy, necroptosis, ferroptosis and pyroptosis | Journal of Neuroinflammation
Langlois JA, Rutland-Brown W, Wald MM. The epidemiology and impact of traumatic brain injury: a brief overview. J Head Trauma Rehabil. 2006;21:375–8. doi.org/10.1097/00001199-200609000-00001. Article PubMed Google Scholar Cao HQ, Dong ED. An update on spinal cord injury research. Neurosci Bull. 2013;29:94–102. doi.org/10.1007/s12264-012-1277-8. Article PubMed Google Scholar O’Donnell MJ, Xavier D,…
Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies
Outcome of DNA sequencing, assembly, and validation In this study, initially total DNA was isolated from the finely chopped, full-grown pupa of Blepharipa sp. The NanoDrop spectrophotometer (1294 ng/μl) and the Qubit fluorometer (732.8 ng/μl) both found that the concentration of total DNA in the sample at an optimum level for mitochondrial DNA enrichment. The Tape Station profile showed…
Bioconductor – adaptest
DOI: 10.18129/B9.bioc.adaptest This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see adaptest. Data-Adaptive Statistics for High-Dimensional Multiple Testing Bioconductor version: 3.11 Data-adaptive test statistics represent a general methodology for performing multiple hypothesis testing on effects sizes while maintaining honest statistical inference when…
H2O is an in-memory platform for distributed, scalable machine learning
H2O is an in-memory platform for distributed, scalable machine learning. H2O uses familiar interfaces like R, Python, Scala, Java, JSON and the Flow notebook/web interface, and works seamlessly with big data technologies like Hadoop and Spark. H2O provides implementations of many popular algorithms such as Generalized Linear Models (GLM), Gradient…
Merging .gam files
Merging .gam files 1 Can anyone point me towards a method to merge gam files that are created by using ‘ vg map ‘ to map illumina reads to my genome graph? I would like to be able to map all of the sequencing runs separately and then merge the…
