Moderator: igor
igor ♦ 12k
- Reputation:
- 11,520
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 8 minutes ago
- Joined:
- 5 years, 7 months ago
- Email:
- i********@hotmail.com
Posts by igor
<prev
• 1,490 results •
page 1 of 149 •
next >
0
votes
0
answers
102
views
0
answers
... Which papers give a different number of genes?
From the paper:
> Gene sets representing PDAC classes were generated by selecting
> significantly upregulated genes in a given class versus all other
> classes. An adjusted P value of 0.01 was used as the cut-off in each
> case.
That seem ...
written 7 days ago by
igor ♦ 12k
1
vote
0
answers
102
views
0
answers
... The genes are in the Supplementary Table 14, which is actually a little confusing because it's an Excel spreadsheet with multiple sheets, so it's not really a single table. ...
written 8 days ago by
igor ♦ 12k
0
votes
0
answers
84
views
0
answers
Comment:
C: Algorithm to remove batch effects
... You may also find this previous discussion helpful: https://www.biostars.org/p/401404/ ...
written 8 days ago by
igor ♦ 12k
0
votes
0
answers
82
views
0
answers
... Isn't this what you are looking for?
> The batch --method wgs option uses the given reference genome’s
> sequencing-accessible regions (“access” BED) as the “targets” – these
> will be calculated on the fly if not provided. No “antitarget” regions
> are used.
...
written 14 days ago by
igor ♦ 12k
0
votes
0
answers
82
views
0
answers
... Did you check the docs? https://cnvkit.readthedocs.io/en/stable/nonhybrid.html ...
written 14 days ago by
igor ♦ 12k
0
votes
2
answers
1.8k
views
2
answers
... That's a helpful video. They also address a lot of other related questions. ...
written 18 days ago by
igor ♦ 12k
0
votes
1
answer
124
views
1
answers
Comment:
C: 10x to cloupe
... The .cloupe file contains additional information that is not available in those three files, so it would not be possible to convert them. ...
written 20 days ago by
igor ♦ 12k
0
votes
2
answers
227
views
2
answers
... > both the STAR and HISAT2 bam files show a large number of mapped reads
> for IFI27
You should check the individual reads. Are they high quality, multi-mappers, etc? Does it look like they are actually mapping properly? ...
written 20 days ago by
igor ♦ 12k
1
vote
2
answers
227
views
2
answers
... > This suggests STAR is either failing to align the relevant reads to IFI27 or failing to count them
Based on the information here, I don't think you can say if STAR is failing or if the other methods are counting problematic reads. ...
written 21 days ago by
igor ♦ 12k
0
votes
1
answer
122
views
1
answers
... > the size of clust_obj is same as sce
The input and output of all those functions is a Seurat object. Most of the size will be due to the expression data which would not change.
> the number of clusters are way more than scanpy provides
Is it using the same resolution?
> seurat documen ...
written 22 days ago by
igor ♦ 12k
Latest awards to igor
Great Question
2 days ago,
created a question with more than 5,000 views.
For Faster BLAST alternative
Teacher
3 days ago,
created an answer with at least 3 up-votes.
For A: .bam files to fastq including the unmapped reads
Great Question
3 days ago,
created a question with more than 5,000 views.
For Faster BLAST alternative
Great Question
12 days ago,
created a question with more than 5,000 views.
For Faster BLAST alternative
Popular Question
24 days ago,
created a question with more than 1,000 views.
For creating visualization tracks for methylation array data
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For A: .bam files to fastq including the unmapped reads
Scholar
4 weeks ago,
created an answer that has been accepted.
For A: Pre-processing MiSeq Paired End data
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For A: .bam files to fastq including the unmapped reads
Popular Question
6 weeks ago,
created a question with more than 1,000 views.
For creating visualization tracks for methylation array data
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: Pre-processing MiSeq Paired End data
Good Question
9 weeks ago,
asked a question that was upvoted at least 5 times.
For Non-computational challenges in bioinformatics
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: .bam files to fastq including the unmapped reads
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: .bam files to fastq including the unmapped reads
Great Question
3 months ago,
created a question with more than 5,000 views.
For Faster BLAST alternative
Great Question
4 months ago,
created a question with more than 5,000 views.
For Faster BLAST alternative
Scholar
6 months ago,
created an answer that has been accepted.
For A: Pre-processing MiSeq Paired End data
Commentator
6 months ago,
created a comment with at least 3 up-votes.
For C: Best Program to use for DE Analysis
Scholar
6 months ago,
created an answer that has been accepted.
For A: Pre-processing MiSeq Paired End data
Commentator
6 months ago,
created a comment with at least 3 up-votes.
For C: Best Program to use for DE Analysis
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: defintion of extremely low coverage
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: .bam files to fastq including the unmapped reads
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: .bam files to fastq including the unmapped reads
Scholar
6 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: 1478 users visited in the last hour