7
votes
6
replies
207
views
2
votes
2
replies
55
views
0
votes
1
reply
41
views
updated 1 hour ago by
Pierre Lindenbaum
165k
•
written 4 hours ago by
slzr_
•
0
0
votes
2
replies
89
views
0
votes
1
reply
60
views
updated 4 hours ago by
GenoMax
150k
•
written 7 hours ago by
umarfaruksahin
•
0
0
votes
0
replies
162
views
835
votes
169
replies
171k
views
110 follow
updated 6 months ago by
Biostar
3.4k
•
written 8.3 years ago by
Istvan Albert
102k
0
votes
0
replies
44
views
11 hours ago by
anna.utili
•
0
0
votes
1
reply
67
views
0
votes
3
replies
165
views
updated 17 hours ago by
Gordon Smyth
★
7.8k
•
written 1 day ago by
Picasa
▴
650
0
votes
3
replies
230
views
3
votes
1
reply
108
views
updated 23 hours ago by
Marcellie87
▴
10
•
written 1 day ago by
Steven
▴
50
0
votes
0
replies
59
views
4
votes
4
replies
1.6k
views
0
votes
0
replies
78
views
1 day ago by
timothy.kirkwood
▴
140
3
votes
0
replies
109
views
1 day ago by
Matthias Zepper
5.1k
0
votes
1
reply
104
views
1
vote
1
reply
117
views
updated 1 day ago by
ATpoint
87k
•
written 1 day ago by
mark.pekarsky
▴
20
1
vote
2
replies
127
views
0
votes
0
replies
78
views
0
votes
0
replies
73
views
0
votes
2
replies
138
views
1
vote
5
replies
277
views
updated 1 day ago by
Pierre Lindenbaum
165k
•
written 2 days ago by
Leane
•
0
0
votes
3
replies
187
views
4
votes
4
replies
320
views
1 day ago by
nigussie.amu
•
0
0
votes
0
replies
121
views
0
votes
0
replies
262
views
2
votes
5
replies
4.1k
views
updated 2 days ago by
Pierre Lindenbaum
165k
•
written 7.6 years ago by
William
★
5.3k
0
votes
0
replies
113
views
0
votes
3
replies
394
views
2
votes
2
replies
1.1k
views
0
votes
0
replies
117
views
updated 1 day ago by
Ram
45k
•
written 2 days ago by
aiswaryabioinfo
▴
30
0
votes
3
replies
186
views
updated 2 days ago by
i.sudbery
21k
•
written 2 days ago by
paguirreazorin
•
0
1
vote
4
replies
318
views
7
votes
5
replies
692
views
0
votes
0
replies
127
views
2 days ago by
rahma.khoualdia
•
0
2
votes
4
replies
282
views
updated 1 day ago by
theHumanBorch
▴
260
•
written 2 days ago by
txema.heredia
▴
210
4
votes
12
replies
7.0k
views
12 follow
updated 2 days ago by
5heikki
11k
•
written 10.3 years ago by
lyz10302012
▴
480
0
votes
2
replies
192
views
2 days ago by
analyst
▴
60
0
votes
1
reply
163
views
0
votes
0
replies
119
views
0
votes
1
reply
156
views
0
votes
0
replies
132
views
updated 2 days ago by
Ram
45k
•
written 2 days ago by
EvoGenExplorer
•
0
2
votes
4
replies
311
views
8
votes
16
replies
608
views
6 follow
0
votes
1
reply
209
views
0
votes
8
replies
424
views
1 day ago by
nmalexan
•
0
0
votes
0
replies
146
views
1
vote
2
replies
344
views
updated 3 days ago by
GenoMax
150k
•
written 3 days ago by
mete.han.celebi
•
0
0
votes
3
replies
231
views
updated 3 days ago by
ATpoint
87k
•
written 3 days ago by
pairedttest
▴
30
Recent Votes
Recent Locations •
All
France/Nantes/Institut du Thorax - INSERM UMR1087, just now
Australia, 17 minutes ago
Mexico, 18 minutes ago
United States, 28 minutes ago
Sweden, 29 minutes ago
Frankrike, 34 minutes ago
United Kingdom, 34 minutes ago
Recent Awards •
All
Popular Question to
sabrilo171
▴
10
Commentator to
ATpoint
87k
Autobiographer to
S.Ghazala
▴
60
Popular Question to
timothy.kirkwood
▴
140
Popular Question to
odi
▴
10
Popular Question to
ecSeq Bioinformatics
▴
10
Scholar to
Devon Ryan
105k
Recent Replies
Comment: Bacterial VCF file annotation using snpEff error
by
1769mkc
★
1.2k
okay I will explore this and update...
Comment: Heatmap problem in R
by
ParastooA
•
0
Just another question
If I want to perferm a data cleaning on Matrix_ series what elements should I consider for doing so?
Comment: Heatmap problem in R
by
ParastooA
•
0
Thanks everyone. yesturday I was a little overwhelmed and now I see your point about sharing the code.
Comment: Coverage depth using samtools
by
Pierre Lindenbaum
165k
yes but the option -b is missing a file if you want to compute all bases overlapping a bed file.
https://www.htslib.org/doc/samtools-depth…
Comment: Bacterial VCF file annotation using snpEff error
by
Pierre Lindenbaum
165k
in https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001884025.1/ and if you look at the files under the FTP tab, you'll see many differen…
Comment: What is the stance on optical duplicates in RNASeq?
by
GenoMax
150k
> but optical ones are a technical artifact
Generally these are applicable only if your data was run on patterned flowcells (which may be …
Comment: Data Integrity (NCBI SRA and TCGA)
by
GenoMax
150k
> I have sequencing data from the NCBI SRAdatabase.
As in raw sequence data from dbGaP and not just counts? So you did get permission to …
Comment: MarkDuplicates RNASeq: A few samples look weird. What could be the cause?
by
GenoMax
150k
Is this different data than what we were discussing in last two questions? Simple explanation may be that the quality of initial RNA was po…
Answer: MarkDuplicates RNASeq: A few samples look weird. What could be the cause?
by
ATpoint
87k
What do you want to do? Differential analysis?
If so, ignore all these lowlevel metrics and see how samples compare in a PCA and how dow…
Comment: Unable to parse config file
by
Phil Ewels
★
1.4k
Agreed, I also just tested it (with the following to try to mimic your setup exactly):
```bash
NXF_VER=24.10.5 nextflow run nf-core/genome…
Comment: Non variants sites of the genome (gVCF file)
by
LauferVA
4.6k
Hi Heureuse ... do you *have* to use a gVCF? Or could you use another format?
Answer: How to rank genes for GSEA using edgeR-LRT results ?
by
Gordon Smyth
★
7.8k
The best choice would be use edgeR's built-in GSEA functionality provided by `camera` and `cameraPR`. These functions adjust for inter-gene…
Comment: How to rank genes for GSEA using edgeR-LRT results ?
by
Gordon Smyth
★
7.8k
Don't necessarily need to run `topTags`. Even with the `glmLRT` output, `lrt` say, the signed LRT statistic
```
z <- sign(lrt$table$logFC) …
Comment: What are the advantages of using the T2T as a reference vs GRCh38 today?
by
Gordon Smyth
★
7.8k
The T2T genome is derived from cell lines of European origin. On digging deeper, we found that the GRCh38 sequences for immunoglobin genes …
Comment: Use limma for correlation analysis of RNA-seqdata and continous trait
by
Gordon Smyth
★
7.8k
The coefficient (logFC) is the log2 expression change for each unit change in the continuous covariate.
The interpretation follows the usu…
Traffic: 1104 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6