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Open Source Biology & Genetics Interest Group

Open source tools and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications.

 Posted in Research

Upstream deletion

 August 18, 2021

Upstream deletion

1



Can anyone please define what is upstream deletion in VCF or guide me towards a link that tells the same


deletion


VCF


upstream

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Can anyone help ??


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This workshop covers basic methods of the image processing and image analysis in R using the Bioconductor package “EBImage” and the Orchestra platform. In addition, the image dataset is obtained from ExperimentHub using the “BioImageDbs” package. Using this dataset, we perform a supervised image segmentation using the U-NET model, one of deep learning models, provided by the rMiW package.


Moderator: 露崎 弘毅 Koki Tsuyuzaki (理化学研究所 RIKEN, 日本 Japan)
Rにおけるバイオ画像解析入門: Introduction to Bioimaging Analysis in R
YouTube Video VVVxYU1TUWRfaC0yRURHc1U2V0RpWDBRLlhXamZHelhsRTVr
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Christophe Vanderaa (UCLouvain, Belgium)
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Moderator: Peter Hickey (Walter and Eliza Hall Institute of Medical Research)
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YouTube Video VVVxYU1TUWRfaC0yRURHc1U2V0RpWDBRLkNMWnhqSUtpa0lV
Visualize Data on Spirals

Zuguang Gu (German Cancer Research Center, Germany)

3:30 PM - 3:55 PM JST (Japan Standard Time) on Thursday, Nov. 4th, 2021
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周烺 Lang Chau (Southern Medical University, China)

4:00 PM - 5:00 PM JST (Japan Standard Time) on Thursday, Nov. 4th, 2021
MANDARIN WORKSHOP

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使用图形语法对MSA进行可视化和注释。
整合MSA图形和其他数据。
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The stacked alignment graphic that represents all individual sequences as rows and homologous residue positions as columns is used almost universally in the visualization of multiple sequence alignment (MSA). We present the R package ggmsa to extend MSA visualization method via integrating stacked MSAs and associated data. Sequence-related data sets such as secondary structures, genes locus, or phenotype are allowed to combining with MSA for exploring the sequence-structure-function relationship. And we developed and integrated multiple alignment visualization methods such as nucleotide difference plots, nucleotide similarity plots, and sequence bundles to exploring multifaceted sequence features from multiple perspectives. The ggmsa package is available at https://github.com/YuLab-SMU/ggmsa.
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Integration of stacked MSAs plot and associated data.
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1:00 PM - 1:40 PM JST (Japan Standard Time) on Thursday, Nov. 4th, 2021
KEYNOTE

Takeya Kasukawa is the team leader of RIKEN Center for Integrative Medical Sciences, Laboratory for Large-Scale Biomedical Data Technology. His major is the development of data management technology that will lead to new discoveries in the field of biomedical science. He has maintained the database of the international collaborative research “FANTOM (Functional ANnoTation of Mammalian Genome) Project”. This database is widely provided to the research community and is expected to contribute to the elucidation of biological phenomena.

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