Moderator: igor
igor ♦ 7.3k
- Reputation:
- 7,260
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 8 hours ago
- Joined:
- 3 years, 7 months ago
- Email:
- i********@hotmail.com
Posts by igor
<prev
• 986 results •
page 1 of 99 •
next >
0
votes
0
answers
101
views
0
answers
... Please refer to these previous discussions:
- https://www.biostars.org/p/160961/
- https://www.biostars.org/p/237547/
...
written 2 days ago by
igor ♦ 7.3k
1
vote
0
answers
122
views
0
answers
... You should use a somatic variant caller rather than trying to overlap variants between different VCFs. Check this similar earlier discussion: https://www.biostars.org/p/175013/
...
written 4 days ago by
igor ♦ 7.3k
0
votes
1
answer
96
views
1
answers
... > Log-fold change does not take into account the variability of the
> change
That may not always be true. For example, the fold change calculated by DESeq2 is "shrunk" using statistical information. ...
written 15 days ago by
igor ♦ 7.3k
1
vote
1
answer
117
views
1
answers
... Different variant have different rules regarding thresholds for counting reads. Additionally, these criteria may vary for different fields. VarScan offers an [explanation on their website][1]:
> VarScan requires that bases meet the minimum Phred quality score
> (default 15 for most commands) ...
written 21 days ago by
igor ♦ 7.3k
0
votes
0
answers
507
views
0
answers
Comment:
C: TCGA expression data (TPM)
... RSEM outputs expected counts, TPMs, and FPKMs. The original post pointed to the counts. ...
written 23 days ago by
igor ♦ 7.3k
0
votes
0
answers
507
views
0
answers
Comment:
C: TCGA expression data (TPM)
... Xena has the raw counts here: https://xenabrowser.net/datapages/?dataset=TCGA-SKCM%2FXena_Matrices%2FTCGA-SKCM.htseq_counts.tsv&host=https%3A%2F%2Fgdc.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443
...
written 23 days ago by
igor ♦ 7.3k
0
votes
3
answers
223
views
3
answers
... The CCA process removes a small fraction of cells. Then, the new matrix is re-scaled. Thus, the values may change. ...
written 29 days ago by
igor ♦ 7.3k
0
votes
3
answers
223
views
3
answers
... There are no "corrected" counts after CCA. CCA is used as an alternate dimensionality reduction. Your Seurat object now has `cca` and `cca.aligned` in the `dr` slot. You can think of it as PCA. After you run PCA, your counts matrix is still the same, but you now have an additional PC matrix.
...
written 4 weeks ago by
igor ♦ 7.3k
0
votes
1
answer
220
views
1
answers
... When you run `FindClusters()`, you specify a resolution. This will determine the number of clusters.
From the [PBMC tutorial][1]:
> The FindClusters function implements the procedure, and contains a
> resolution parameter that sets the ‘granularity’ of the downstream
> clustering, with in ...
written 7 weeks ago by
igor ♦ 7.3k
1
vote
2
answers
693
views
2
answers
... Variants from RNA-seq is a controversial topic. Although there are arguments against (as other have already mentioned), it's also not entirely unreasonable. There is an interesting statement from [Coudray et al][1] (where they also make some pipeline recommendations):
> The overlap between RNA-s ...
written 8 weeks ago by
igor ♦ 7.3k
Latest awards to igor
Good Answer
2 days ago,
created an answer that was upvoted at least 5 times.
For A: read length of sequence
Appreciated
4 days ago,
created a post with more than 5 votes.
For A: Must know algorithms before attending a bioinformatics interview
Teacher
20 days ago,
created an answer with at least 3 up-votes.
For A: GL000201,GL000202... etc What are these?
Scholar
20 days ago,
created an answer that has been accepted.
For A: Pre-processing MiSeq Paired End data
Popular Question
28 days ago,
created a question with more than 1,000 views.
For Why are there multiple GFP nucleotide sequences?
Popular Question
4 weeks ago,
created a question with more than 1,000 views.
For Why are there multiple GFP nucleotide sequences?
Scholar
6 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: GL000201,GL000202... etc What are these?
Popular Question
6 weeks ago,
created a question with more than 1,000 views.
For Why are there multiple GFP nucleotide sequences?
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: Pre-processing MiSeq Paired End data
Popular Question
7 weeks ago,
created a question with more than 1,000 views.
For Why are there multiple GFP nucleotide sequences?
Appreciated
8 weeks ago,
created a post with more than 5 votes.
For A: Must know algorithms before attending a bioinformatics interview
Teacher
10 weeks ago,
created an answer with at least 3 up-votes.
For A: GL000201,GL000202... etc What are these?
Teacher
10 weeks ago,
created an answer with at least 3 up-votes.
For A: GL000201,GL000202... etc What are these?
Scholar
10 weeks ago,
created an answer that has been accepted.
For A: Pre-processing MiSeq Paired End data
Student
11 weeks ago,
asked a question with at least 3 up-votes.
For smoothing or binning bigWig file
Scholar
12 weeks ago,
created an answer that has been accepted.
For A: Pre-processing MiSeq Paired End data
Teacher
12 weeks ago,
created an answer with at least 3 up-votes.
For A: GL000201,GL000202... etc What are these?
Great Question
3 months ago,
created a question with more than 5,000 views.
For Faster BLAST alternative
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: GL000201,GL000202... etc What are these?
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Why are there multiple GFP nucleotide sequences?
Appreciated
3 months ago,
created a post with more than 5 votes.
For A: Must know algorithms before attending a bioinformatics interview
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar
3 months ago,
created an answer that has been accepted.
For A: Pre-processing MiSeq Paired End data
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: 1362 users visited in the last hour