User: shoujun.gu

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shoujun.gu310
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1 year, 4 months ago
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Posts by shoujun.gu

<prev • 97 results • page 2 of 10 • next >
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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 8 months ago by shoujun.gu310
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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 8 months ago by shoujun.gu310
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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 9 months ago by shoujun.gu310
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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 9 months ago by shoujun.gu310
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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 9 months ago by shoujun.gu310
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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 10 months ago by shoujun.gu310
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Comment: C: Remove character from Fasta IDs -- python
... You can use a list to collect all the corrected lines first, then write them into a file. ...
written 10 months ago by shoujun.gu310
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Comment: C: How to extract upstream and downstream sequence of a set of genes using python
... I recently did the same work. And the lesson I learned is get the fasta and annotation files from the SAME source (eg, gencode). Do not fully trust the version number... And even though, I found the sequences I extracted from some genes are not completely consistent with the annotation from NCBI ge ...
written 10 months ago by shoujun.gu310
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Comment: C: Need some help regarding Deep Learning/Python/TensorFlow
... "ValueError: Error when checking input: expected input.cell.expression to have shape (942,) but got array with shape (17743,)". My guess is that the model only used 942 genes for training, and here you provided 17743 genes for prediction, which caused this input error. ...
written 10 months ago by shoujun.gu310
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Comment: C: gff3 header delimiter space or a tab
... Yes, I just realize the post is deal with the header only. ...
written 10 months ago by shoujun.gu310

Latest awards to shoujun.gu

Scholar 11 months ago, created an answer that has been accepted. For A: about batch correction in scRNA-seq
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: about batch correction in scRNA-seq

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