User: shoujun.gu

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shoujun.gu310
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Posts by shoujun.gu

<prev • 97 results • page 1 of 10 • next >
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Comment: C: Result of scanpy tools rank_genes_groups
... In the source code, 'rank_genes_groups' uses stats.ttest_ind_from_stats() for default method, which returns t-statistics. You may double check the value of your adata.shape[1], or try using something like adata.raw.shape[1] or adata.X.toarray().shape[1]. ...
written 3 months ago by shoujun.gu310
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Comment: C: Result of scanpy tools rank_genes_groups
... The default setting of "tl.rank_genes_groups" is to return top 100 marker gene. I think all positive z-score is expected. ...
written 3 months ago by shoujun.gu310
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Comment: C: Result of scanpy tools rank_genes_groups
... What makes you think 1.2 to 39 doesn't make sense for z-score? ...
written 3 months ago by shoujun.gu310
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Comment: C: about batch correction in scRNA-seq
... I think most of the batch correct algo are over-processing/ over-normalizing the data. They are implicitly assume some situations, such as scRNASeq data are neighboring graph, etc, while many real life data may not satisfied. And people should accept the fact that not all samples could be merged. ...
written 4 months ago by shoujun.gu310
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Comment: C: Seurat FeaturePlot: highlight only cells coexpressing several genes
... Not sure how to do it in Seurat. But this kind of work could be done by general data analysis process. ...
written 4 months ago by shoujun.gu310
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Comment: A: pwm matrix from txt file python
... 1. str.split() returns a list. That's why you get list. 2. use pandas to work with table in python. ...
written 4 months ago by shoujun.gu310
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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 7 months ago by shoujun.gu310
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Comment: C: How to read vcf file in python?
... I always read it by pandas (after removing the heads). ...
written 7 months ago by shoujun.gu310
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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 7 months ago by shoujun.gu310
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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 7 months ago by shoujun.gu310

Latest awards to shoujun.gu

Scholar 10 months ago, created an answer that has been accepted. For A: about batch correction in scRNA-seq
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: about batch correction in scRNA-seq

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