User: xiaoguang
xiaoguang • 20
- Reputation:
- 20
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- 2 days, 10 hours ago
- Joined:
- 12 months ago
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Posts by xiaoguang
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... The SCENIC package is software for the analysis of transcription factor activity and localized genes in single-cell transcriptome sequencing data, and the R package also scores the transcription factor activity of each cell.
can I use the pack for bulk seq? ...
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6
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... Is there any tutorial for X! Tandem software, I have n’t found it for a long time ...
written 12 weeks ago by
xiaoguang • 20
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... ![enter image description here][1]
> This picture expresses the ligand and receptor interaction between cells. Color represents cell classification and gray represents gene expression. How can this graph be drawn?
[1]: https://cdn.webchain.site/file/imgdisk-2/2020/03/09/hshs2019366946d27f67. ...
written 3 months ago by
xiaoguang • 20
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5 follow
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... There is a question about `Seurat` that has been bothering me all the time. I would like to ask your opinions. For the case of multiple samples, In order to eliminate the batch effect, `Seurat` clustering will choose to integrate multiple samples, which is no problem. But when searching for markers, ...
written 4 months ago by
xiaoguang • 20
• updated
3 months ago by
Friederike ♦ 5.7k
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... Thank you very much! ...
written 5 months ago by
xiaoguang • 20
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... When `monocle3` was used to calculate the pseudotime of 170,000 cells, `cds <-learn_graph(cds)`was run, but after calculating a few rounds, the error message was displayed as :
```
*** caught segfault ***
address 0x2b3ae695f5c0, cause 'memory not mapped'
Traceback:
1: .Call("R_euclidean_dist", ...
written 5 months ago by
xiaoguang • 20
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... I use the latest version of **monocle3** and follow the official tutorial to calculate the *pseudotime* ,but since there are two **partitions** in the calculation result, when I set the root node, half of my pseudotime is always gray. How can I do this for all Cell calculates pseudo time?
my code i ...
written 6 months ago by
xiaoguang • 20
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1
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... How to get an exact match from the bam comparison file, it is well known that M in the cigar character is completely consistent or there is mismatch, but how do I get a completely consistent sequence? ...
written 11 months ago by
xiaoguang • 20
• updated
10 months ago by
yasokannan93 • 20
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... If we use featurecount, we can get gens quantification beacuse of aligning sequences to genome, but we use Salmon, we only get isoforms quantification.
however,TPM is the percentage of FPKM,Are they different？ ...
written 11 months ago by
xiaoguang • 20
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555
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... Is there any R packages or programs could help me to calculate **effective length** of every isoform or gene?
We know the importance of effective length when we calculate TPM for isoforms or genes . but we can not got it from featurecount program. Salmon can get it ,but it is only for ...
written 11 months ago by
xiaoguang • 20
• updated
10 months ago by
Gordon Smyth • 1.7k
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