User: shoujun.gu

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shoujun.gu290
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Posts by shoujun.gu

<prev • 91 results • page 1 of 10 • next >
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Comment: C: Getting the cells from the clusters Seurat has found
... you can plot the known marker gene to check the cluster. ...
written 12 weeks ago by shoujun.gu290
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Comment: C: How to read vcf file in python?
... I always read it by pandas (after removing the heads). ...
written 12 weeks ago by shoujun.gu290
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Comment: C: Down regulated genes in sC-RANseq
... All analysis serves to your project goal. It all depends on what information you are trying to extract, and whether it is required for supporting your hypothesis. ...
written 12 weeks ago by shoujun.gu290
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Comment: C: scRNA-seq analysis : the IDENTITY of the CLUSTERS across MULTIPLE EXPERIMENTS
... In general: 1. For most (if not all) unsupervised clustering algo, cluster numbers can be arbitrarily determined by adjusting algo params. Therefore, you can always keep any cluster number you want. However, packaged analysis platforms (such as seurat) may or may not provide the access to fine tun ...
written 12 weeks ago by shoujun.gu290
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Comment: C: Plotting - taking size and mean in consideration
... Any plot that can represent 3 features will be fine, such as colored scatter plot (x: mean; y: size; dot color: exon), etc. ...
written 3 months ago by shoujun.gu290
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Comment: C: Support vector machine apply on gene expression data
... SVM is just a ML method. There is no so called correct matrix. ...
written 3 months ago by shoujun.gu290
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Comment: C: scRNA-seq and the batch effects
... I have tried couple methods. The biggest problem I found is, since you have no idea what's the real data suppose to be, there is no way you can really measure the accuracy of these methods. If I have to pick one to use, I will choose MNN or Scanorama (but most of the time, I prefer not to torture t ...
written 3 months ago by shoujun.gu290
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Comment: C: Seurat Cluster Low MT Genes
... I always use a fixed percentage (such as 10%), since high MT% may indicate dying cells. See: https://kb.10xgenomics.com/hc/en-us/articles/360001086611-Why-do-I-see-a-high-level-of-mitochondrial-gene-expression- ...
written 3 months ago by shoujun.gu290
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Comment: C: Seurat Cluster Low MT Genes
... It depends on how your samples are prepared. Usually, sNucSeq samples has much lower MT% than scRNASeq samples. ...
written 3 months ago by shoujun.gu290
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Comment: C: Combining files based on chromosome and position next to each other - column vi
... I don't think there are some one-click tools can do this job. It may require some coding work to do this task, python, R , etc . ...
written 5 months ago by shoujun.gu290

Latest awards to shoujun.gu

Scholar 6 months ago, created an answer that has been accepted. For A: about batch correction in scRNA-seq
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: about batch correction in scRNA-seq

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