User: tujuchuanli

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tujuchuanli90
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Posts by tujuchuanli

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Answer: A: How to identify down-regulated genes in monocle
... Does anyone know how to identify down-regulated genes by monocle? ...
written 8 months ago by tujuchuanli90
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How to identify down-regulated genes in monocle
... Hi, all Here I used “differentialGeneTest” in monocle to identify differentially expressed genes (DEGs) when analyzing scRNA-seq data. My question is how to mark up/down-regulated genes or there are only up-regulated genes to be identified when using “differentialGeneTest” in monocle? If so how do ...
scrna-seq monocle degs written 8 months ago by tujuchuanli90
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Comment: C: How to classify cells based on the expression of genes in scRNA-seq
... Thank you for helpful replying, There are about 15 paralogs for gene E and 8 paralogs in these are active paralogs. Although the enzyme activity of these 8 paralogs could not be the same. Summing up across these active paralogs could be the best way for me. I don`t expect that cells with high expr ...
written 8 months ago by tujuchuanli90
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Comment: C: How to classify cells based on the expression of genes in scRNA-seq
... Thanks, I have edited my post. There are many members for gene E in human genome. Maybe I can call it isoform. However, I don`t mean that these members were generated by different alternative splicing from the same pre-mRNA. ...
written 8 months ago by tujuchuanli90
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How to classify cells based on the expression of genes in scRNA-seq
... Hi, I am analyzing the scRNA-seq data for breast cancer. Here I want to classify the cells into E+ and E- group which is based on the expression level of gene E (cells with low expression of gene E is E- and cells with high expression of gene E is E+). However, there are several members (isoforms) ...
scrna-seq expression written 8 months ago by tujuchuanli90
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Is the upregulation of ribosome genes in scRNA-seq reliable?
... Hi all, I am analyzing the scRNA-seq data in Breast cancer. I find that there are 7 clusters in my dataset. I determined cells in these 7 clusters as luminal epithelial cells by expression of marker genes. In one of these clusters, I find that some of ribosome genes are up-regulated when comparing ...
scrna-seq ribosome gene rna-seq written 9 months ago by tujuchuanli90
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Comment: C: Question about scRNA-seq analysis
... Thanks, benformatics Actually, I have written a letter to the author and still not have response. However, if they noticed something and excluded it from subsequent analysis, there should be 12 samples instead of 13 samples which were the sample number mentioned in the paper. ...
written 10 months ago by tujuchuanli90
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Question about scRNA-seq analysis
... Hi, I am interested in the scRNA-seq data from a previous study (http://www.ncbi.nlm.nih.gov/pubmed/31067475). They deposited the dataset under the accession “GSE134520” in GEO dataset. Since they didn`t provide the raw data generated from cellranger, I re-run the cellranger pipeline and do the sub ...
scrna-seq written 10 months ago by tujuchuanli90
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Comment: C: Question about the type of SRA data (SRR9713131, single- or pair-end?)
... Do you mean that I need all of three files to run "cellranger count"? The other data in the same dataset, such as "https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR9713123#", contains only two files and the running of cellranger count is just fine using these two files. Why I use all the three fi ...
written 11 months ago by tujuchuanli90
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Comment: C: Question about the type of SRA data (SRR9713131, single- or pair-end?)
... Hi, ale_abd, Thank you for your replying. Actually, I tried to convert it from SRA-format to fastq-format using fastq-dump with --split-files. However, it came out to be single-end. Next, if you click the **“Reads” tab** on page https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR9713131. You will f ...
written 11 months ago by tujuchuanli90

Latest awards to tujuchuanli

Popular Question 4 months ago, created a question with more than 1,000 views. For raw counts in TCGA RNA-seq data
Popular Question 7 months ago, created a question with more than 1,000 views. For raw counts in TCGA RNA-seq data
Popular Question 10 months ago, created a question with more than 1,000 views. For question about survival analysis using TCGA dataset
Popular Question 11 months ago, created a question with more than 1,000 views. For question about survival analysis using TCGA dataset
Popular Question 11 months ago, created a question with more than 1,000 views. For Correlation between gene expression and methylation
Popular Question 22 months ago, created a question with more than 1,000 views. For Correlation between gene expression and methylation

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