Shankar K Shakya Ph.D. (@shakya) header
Shankar K Shakya Ph.D. (@shakya) profile picture

Bioinformatics Scientist @BallHort #USAIDfellow #Rstats. Ph.D. from @PhytophthoraLab. Alumni @OregonState @UF #firstgen from🇳🇵

Greater Chicago area
Joined July 2011
Photo by Shankar K Shakya Ph.D. (@shakya)Photo by Shankar K Shakya Ph.D. (@shakya)Photo by Shankar K Shakya Ph.D. (@shakya)Photo by Shankar K Shakya Ph.D. (@shakya)Photo by Shankar K Shakya Ph.D. (@shakya)Photo by Shankar K Shakya Ph.D. (@shakya)Photo by Shankar K Shakya Ph.D. (@shakya)Photo by Shankar K Shakya Ph.D. (@shakya)Photo by Shankar K Shakya Ph.D. (@shakya)Photo by Shankar K Shakya Ph.D. (@shakya)
Abstract done for #PAG32. If you are interested working in ornamental industry, come find me at the trees and shrubs session on day1.
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The 10 types of clustering that all data scientists need to know. Let's dive in: 1. K-Means Clustering: This is a centroid-based algorithm, where the goal is to minimize the sum of distances between points and their respective cluster centroid. 2. Hierarchical Clustering: This method creates a tree of clusters. It is subdivided into Agglomerative (bottom-up approach) and Divisive (top-down approach). 3. DBSCAN (Density-Based Spatial Clustering of Applications with Noise): This algorithm defines clusters as areas of high density separated by areas of low density. 4. Mean Shift Clustering: It is a centroid-based algorithm, which updates candidates for centroids to be the mean of points within a given region. 5. Gaussian Mixture Models (GMM): This method uses a probabilistic model to represent the presence of subpopulations within an overall population without requiring to assign each data point to a cluster. 6. Spectral Clustering: It uses the eigenvalues of a similarity matrix to reduce dimensionality before applying a clustering algorithm, typically K-means. 7. OPTICS (Ordering Points To Identify the Clustering Structure): Similar to DBSCAN, but creates a reachability plot to determine clustering structure. 8. Affinity Propagation: It sends messages between pairs of samples until a set of exemplars and corresponding clusters gradually emerges. 9. BIRCH (Balanced Iterative Reducing and Clustering using Hierarchies): Designed for large datasets, it incrementally and dynamically clusters incoming multi-dimensional metric data points. 10. CURE (Clustering Using Representatives): It identifies clusters by shrinking each cluster to a certain number of representative points rather than the centroid. There you have it- my top 10 types of clustering every data scientist needs to know. The next problem you'll face is how to apply them to data science to business. I'd like to help. I’ve spent 100 hours consolidating my learnings into a free 5-day course, How to Solve Business Problems with Data Science. It comes with: 300+ lines of R and Python code 5 bonus trainings 2 systematic frameworks 1 complete roadmap to avoid mistakes and start solving business problems with data science, TODAY. 👉 Here it is for free: learn.business-science.io/fr…
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FLAIR2: Detecting haplotype-specific transcript variation in long reads genomebiology.biomedcentral.…
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Two papers in @Nature present a new genome editing technique that enables the insertion, inversion and deletion of long DNA sequences at user-specified genome positions. The approach may provide an easier method of genome editing. go.nature.com/3RGkI8M go.nature.com/3RHBvIs
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Genome assembly Tutorials with SPades- Paired-end Illumina Reads
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Attending summer institute of statistical genetics at @KendedaBuilding @GeorgiaTech this week. Any twitter friends around here!!!
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We are excited to announce cleaner nucleotide (nt) and protein (nr) BLAST databases with more accurate results! We now use NCBI quality assurance tools to systematically remove misleading sequences. Learn more: ow.ly/CEk950RlpoM #NCBICGR
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HiFi assembler folks, if you have tons of raw fasta (total 700Gb) files as input but limited by the RAM whats the path you have taken to perform an assembly. Asking for a friend.
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Shankar K Shakya Ph.D. retweeted
REVIEW: Reflections on the ABC model of flower development (John L Bowman, Edwige Moyroud) buff.ly/3OIDlHM @ASPB #PlantSci
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Why?
PSA, since I've now seen problems arising from this: As of Sept 2023, GATK no longer makes missing genotypes explicit in VCFs (i.e. "./." as in the VCF spec). Missing genotypes are instead coded as "0/0" with a DP=0 format field. See attached for examples.
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Want to learn about the latest updates we've made to enhance the options available when you're using the custom annotation option in the Variant Effect Predictor? Read more in our latest blog post: 👉 ensembl.info/2024/01/26/cool… #genomics #bioinformatics #VEP 🧬
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🧑‍💻 Happy to announce that sandbox.bio v2 has been released! Same bioinformatics tutorials, but now powered by Linux running in your browser. Stay tuned, we'll be adding lots more tutorials this year.
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I don't understant how people still use t.test(), aov(), wilcox.test() and kruskal.test() in 2023 & put them into R books, when there is ggbetweenstats() available from {ggstatsplot} package? It's time to move on! R progressed! indrajeetpatil.github.io/ggs… #rstats #rstudio #r4ds
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cgMSI: pathogen detection within species from nanopore metagenomic sequencing data bmcbioinformatics.biomedcent…
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🔬 Exciting news! We've just created a list of bioinformatics conferences, filling a gap that's been missing for years. It's a handy resource for planning your 2024 conference schedule. Check it out here: lskatz.github.io/posts/2023/… 🗓️ #Bioinformatics #ConferenceList
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The Ball Helix Bioengineering team is looking for a dedicated and passionate Bioengineering Scientist to work with our team in developing innovative products for the ornamental industry. Join our team and help us continue to #ColorTheWorld! 🌻🌹🌸🪻linkedin.com/jobs/view/37191…
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