User: shoujun.gu

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shoujun.gu250
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Posts by shoujun.gu

<prev • 82 results • page 1 of 9 • next >
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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 4 days ago by shoujun.gu250
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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 6 days ago by shoujun.gu250
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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 6 days ago by shoujun.gu250
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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 6 days ago by shoujun.gu250
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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 8 days ago by shoujun.gu250
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Answer: A: gff3 header delimiter space or a tab
... gff3 from gencode is tab. edit: sorry, I didn't notice the post is talk about the header... Then it just regular sentences I think. ...
written 8 days ago by shoujun.gu250
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Comment: C: deep learning predict gene expression
... No ml tools can do these tasks now. You may develop one by your own.. ...
written 14 days ago by shoujun.gu250
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Answer: C: How to grab a column out of pandas data frame for encoding
... modify line7 to : encoded.extend(freqs.split('\n')) ...
written 15 days ago by shoujun.gu250
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Comment: C: Algorithm for clustering single cells based on SNPs?
... Shouldn't it contain the batch information in the Seurat object? And 10X is 3' sequence, I am not sure whether you could analyze SNP on these data. ...
written 21 days ago by shoujun.gu250
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Comment: C: What to think about when treating scRNA-Seq data as bulk RNA-Seq data
... You can use scDE tools, such as DESingle, etc. Bulk analysis usually do not consider dropouts. ...
written 22 days ago by shoujun.gu250

Latest awards to shoujun.gu

Scholar 5 weeks ago, created an answer that has been accepted. For A: about batch correction in scRNA-seq
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: about batch correction in scRNA-seq

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