Moderator: igor
igor ♦ 10k
- Reputation:
- 10,320
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 6 hours ago
- Joined:
- 4 years, 11 months ago
- Email:
- i********@hotmail.com
Posts by igor
<prev
• 1,309 results •
page 1 of 131 •
next >
0
votes
0
answers
70
views
0
answers
Comment:
C: Very low probability densities
... Why do you think they are low? Your chromosome has millions of bases, but you only have values for about a thousand of them. In other words, most values are 0, so the average should be very low. ...
written 6 hours ago by
igor ♦ 10k
0
votes
2
answers
57
views
2
answers
... > So is it possible to get TPM or even FPKM matrix from raw count martix?
DESeq2 has the `fpkm()` function specifically for that.
If you just want TPMs and keep things simple, you could also just download them from [Xena][1].
[1]: https://xenabrowser.net/datapages/?host=https%3A%2F%2Ftoil.x ...
written 23 hours ago by
igor ♦ 10k
0
votes
2
answers
85
views
2
answers
... You can try [KEGGgraph][1], which downloads directly from KEGG, so you end up with the current version.
[1]: https://www.bioconductor.org/packages/release/bioc/html/KEGGgraph.html ...
written 1 day ago by
igor ♦ 10k
0
votes
1
answer
98
views
1
answers
... If you cannot remove that study, does it mean it has information that the other studies don't? In that case, that study has 2 different variables (that and the batch), so you don't know how much each is contributing. ...
written 2 days ago by
igor ♦ 10k
0
votes
2
answers
85
views
2
answers
Comment:
C: Using limma for scRNAseq data
... You could also treat the replicates as a covariate. ...
written 2 days ago by
igor ♦ 10k
0
votes
1
answer
98
views
1
answers
... If that one study is very important and you cannot remove it, then how can you comment on or correct the batch effect? There is only a single batch. ...
written 2 days ago by
igor ♦ 10k
0
votes
1
answer
1.3k
views
1
answers
Comment:
C: GSEA with mouse RNAseq data
... MSigDB pathways are presented as human symbols, but are based on multiple species.
Related discussion: https://www.biostars.org/p/147484/ ...
written 2 days ago by
igor ♦ 10k
2
votes
2
answers
85
views
2
answers
... The best source for KEGG pathways should be KEGG itself. Other sources may be outdated or have some restrictions.
MSigDB support forum had a nice [explanation][1]:
> For the Reactome database, the information you found in the release
> notes is correct - it is based on Reactome version 44. W ...
written 2 days ago by
igor ♦ 10k
0
votes
2
answers
85
views
2
answers
Comment:
C: Using limma for scRNAseq data
... Maybe you don't really need to reinvent the wheel. Something like the t-test or the Wilcoxon test have been used for all sorts of data over many years. The advantage of a generic test is that it is generic. ...
written 2 days ago by
igor ♦ 10k
1
vote
2
answers
85
views
2
answers
Answer:
A: Using limma for scRNAseq data
... [Soneson et al][1] compared a few different methods, including limma, so it's certainly possible:
![enter image description here][2]
[1]: https://doi.org/10.1038/nmeth.4612
[2]: https://media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fnmeth.4612/MediaObjects/41592_2018_Art ...
written 5 days ago by
igor ♦ 10k
Latest awards to igor
Scholar
2 days ago,
created an answer that has been accepted.
For A: Pre-processing MiSeq Paired End data
Popular Question
12 days ago,
created a question with more than 1,000 views.
For methylation array group probes
Scholar
16 days ago,
created an answer that has been accepted.
For A: Pre-processing MiSeq Paired End data
Commentator
17 days ago,
created a comment with at least 3 up-votes.
For C: Best Program to use for DE Analysis
Popular Question
20 days ago,
created a question with more than 1,000 views.
For methylation array group probes
Popular Question
21 days ago,
created a question with more than 1,000 views.
For find motif locations in the genome
Teacher
22 days ago,
created an answer with at least 3 up-votes.
For A: .bam files to fastq including the unmapped reads
Cylon
4 weeks ago,
received 1,000 up votes.
Good Answer
4 weeks ago,
created an answer that was upvoted at least 5 times.
For A: read length of sequence
Scholar
5 weeks ago,
created an answer that has been accepted.
For A: Pre-processing MiSeq Paired End data
Popular Question
5 weeks ago,
created a question with more than 1,000 views.
For find motif locations in the genome
Scholar
5 weeks ago,
created an answer that has been accepted.
For A: Pre-processing MiSeq Paired End data
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: .bam files to fastq including the unmapped reads
Great Question
7 weeks ago,
created a question with more than 5,000 views.
For Faster BLAST alternative
Popular Question
7 weeks ago,
created a question with more than 1,000 views.
For find motif locations in the genome
Popular Question
10 weeks ago,
created a question with more than 1,000 views.
For find motif locations in the genome
Good Answer
12 weeks ago,
created an answer that was upvoted at least 5 times.
For A: read length of sequence
Teacher
12 weeks ago,
created an answer with at least 3 up-votes.
For A: .bam files to fastq including the unmapped reads
Good Answer
3 months ago,
created an answer that was upvoted at least 5 times.
For A: read length of sequence
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: .bam files to fastq including the unmapped reads
Good Question
3 months ago,
asked a question that was upvoted at least 5 times.
For ATAC-seq peak calling with MACS
Appreciated
3 months ago,
created a post with more than 5 votes.
For A: Must know algorithms before attending a bioinformatics interview
Student
3 months ago,
asked a question with at least 3 up-votes.
For Non-computational challenges in bioinformatics
Commentator
3 months ago,
created a comment with at least 3 up-votes.
For C: Best Program to use for DE Analysis
Scholar
3 months ago,
created an answer that has been accepted.
For A: Pre-processing MiSeq Paired End data
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1417 users visited in the last hour