Shankar K Shakya Ph.D.
@shakya
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Bioinformatics Scientist @BallHort #USAIDfellow #Rstats. Ph.D. from @PhytophthoraLab. Alumni @OregonState @UF #firstgen from🇳🇵
Greater Chicago area
Joined July 2011
Our Petunia hybrida genome paper is now on @biorxivpreprint. This was a collaborative project between @BallHort @Ball_Helix and Plant & Food research group of New Zealand. https://t.co/FFv5cnYkK4
biorxiv.org
Petunia hybrida is the world’s most popular garden plant and is regarded as a supermodel for studying the biology associated with the Asterid clade, the largest of the two major groups of flowering...
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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
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FLAIR2: Detecting haplotype-specific transcript variation in long reads https://t.co/LMSaVlwMI3
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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. https://t.co/EwMQtgoTrE
https://t.co/ecUGLy4l2O
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Generalized linear mixed models (GLMMs) are critically important for the analysis of non-normal data. Check out our recent review article to learn more. https://t.co/3tX0dJOPka
frontiersin.org
Modern data analysis typically involves the fitting of a statistical model to data, including the estimation of model parameters and their precision (standar...
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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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Krisp: A Python package to aid in the design of CRISPR and amplification-based diagnostic assays from WGS data https://t.co/c8bI0bq1ds 🧬🖥️ https://t.co/vTtJM8I9H6 🐍
pypi.org
A lightweight tool for finding diagnostic regions in whole genome data
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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: https://t.co/sjtStUnJFi
#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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REVIEW: Reflections on the ABC model of flower development (John L Bowman, Edwige Moyroud) https://t.co/7fINcVP2SI
@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: 👉 https://t.co/CTf89sICTt
#genomics #bioinformatics #VEP 🧬
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BCFtools/liftover: bcftools plugin to convert genetic variants across genome assemblies https://t.co/ZTIUbaLHlC 🧬🖥️
academic.oup.com
AbstractMotivation. Many genetics studies report results tied to genomic coordinates of a legacy genome assembly. However, as assemblies are updated and im
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🧑💻 Happy to announce that https://t.co/3DKXXBduDD 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! https://t.co/6LARpMiaCe
#rstats #rstudio #r4ds
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cgMSI: pathogen detection within species from nanopore metagenomic sequencing data https://t.co/zAkMv2TBB8
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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: https://t.co/9KAvqdAd3W 🗓️ #Bioinformatics #ConferenceList
lskatz.github.io
Every fiscal year, we have to predict where we are going to travel over the whole next year. However, conferences mainly post on their own website, making no real central place where you can search...
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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! 🌻🌹🌸🪻 https://t.co/2coGeAmY3n
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