User: tujuchuanli
tujuchuanli • 90
- Reputation:
- 90
- Status:
- Trusted
- Location:
- Last seen:
- 3 months, 3 weeks ago
- Joined:
- 2 years, 7 months ago
- Email:
- t**********@163.com
Posts by tujuchuanli
<prev
• 77 results •
page 1 of 8 •
next >
0
votes
1
answer
253
views
1
answers
... Does anyone know how to identify down-regulated genes by monocle? ...
written 8 months ago by
tujuchuanli • 90
0
votes
1
answer
253
views
1
answer
... 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 ...
written 8 months ago by
tujuchuanli • 90
0
votes
0
answers
254
views
0
answers
... 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
tujuchuanli • 90
0
votes
0
answers
254
views
0
answers
... 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
tujuchuanli • 90
0
votes
0
answers
254
views
0
answers
... 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) ...
written 8 months ago by
tujuchuanli • 90
1
vote
0
answers
1.5k
views
0
answers
... 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 ...
written 9 months ago by
tujuchuanli • 90
0
votes
0
answers
255
views
0
answers
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
tujuchuanli • 90
0
votes
0
answers
255
views
0
answers
... 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 ...
written 10 months ago by
tujuchuanli • 90
0
votes
1
answer
561
views
1
answers
... 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
tujuchuanli • 90
0
votes
1
answer
561
views
1
answers
... 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
tujuchuanli • 90
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
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 965 users visited in the last hour