updated 8 days ago by
zx8754
11k
•
written 8 days ago by
sidrah.maryam
▴
50
0
votes
0
replies
94
views
0
votes
1
reply
147
views
1
vote
0
replies
234
views
0
votes
0
replies
103
views
2
votes
2
replies
119
views
updated 8 days ago by
Pierre Lindenbaum
154k
•
written 8 days ago by
MobiusT
▴
10
0
votes
1
reply
151
views
updated 7 days ago by
Ram
39k
•
written 8 days ago by
chengc2016zzu
•
0
0
votes
0
replies
85
views
1
vote
2
replies
207
views
0
votes
0
replies
121
views
0
votes
0
replies
119
views
updated 8 days ago by
GenoMax
129k
•
written 8 days ago by
keiko.asakura
•
0
0
votes
2
replies
226
views
0
votes
2
replies
206
views
updated 8 days ago by
Ram
39k
•
written 9 days ago by
Joel Wallenius
▴
130
1
vote
3
replies
704
views
0
votes
1
reply
172
views
updated 7 days ago by
Ram
39k
•
written 9 days ago by
barrypraveen
▴
110
0
votes
2
replies
178
views
0
votes
1
reply
140
views
0
votes
0
replies
101
views
0
votes
3
replies
230
views
updated 7 days ago by
Ram
39k
•
written 9 days ago by
abbas.waseem.gcu
▴
20
0
votes
1
reply
189
views
0
votes
1
reply
181
views
updated 9 days ago by
Pierre Lindenbaum
154k
•
written 9 days ago by
MobiusT
▴
10
0
votes
4
replies
293
views
9 days ago by
Ahmad
▴
10
0
votes
2
replies
252
views
0
votes
6
replies
342
views
9 days ago by
hasani.iut6
▴
60
1
vote
2
replies
267
views
0
votes
0
replies
178
views
7 days ago by
Vincent Laufer
★
2.9k
0
votes
1
reply
246
views
updated 9 days ago by
Fabio Marroni
★
3.0k
•
written 10 days ago by
1362321710
•
0
1
vote
1
reply
232
views
updated 10 days ago by
Pierre Lindenbaum
154k
•
written 10 days ago by
mathalfilip
•
0
0
votes
1
reply
240
views
updated 10 days ago by
Mensur Dlakic
★
23k
•
written 11 days ago by
abhiramiabhirami9072
•
0
2
votes
5
replies
418
views
8 days ago by
DanielEB_fisk
▴
10
0
votes
0
replies
197
views
1
vote
0
replies
259
views
0
votes
1
reply
767
views
updated 7 days ago by
Joe
21k
•
written 11 days ago by
Aatif Hashmi
•
0
0
votes
1
reply
304
views
updated 11 days ago by
Vincent Laufer
★
2.9k
•
written 11 days ago by
Sara
▴
10
1
vote
2
replies
271
views
0
votes
2
replies
296
views
4
votes
4
replies
360
views
updated 7 days ago by
Joe
21k
•
written 12 days ago by
antoine.fauchois92
▴
20
0
votes
0
replies
162
views
12 days ago by
ahmadjoyyia
▴
10
0
votes
0
replies
183
views
updated 11 days ago by
Ram
39k
•
written 12 days ago by
txema.heredia
▴
70
1
vote
1
reply
236
views
0
votes
2
replies
301
views
23 hours ago by
zhangdengwei
▴
190
0
votes
1
reply
208
views
0
votes
0
replies
165
views
0
votes
0
replies
146
views
0
votes
2
replies
275
views
0
votes
1
reply
208
views
updated 12 days ago by
Vincent Laufer
★
2.9k
•
written 12 days ago by
Saran
▴
20
1
vote
1
reply
173
views
1
vote
1
reply
155
views
1
vote
2
replies
228
views
12 days ago by
Prangan
▴
20
0
votes
0
replies
113
views
0
votes
2
replies
197
views
12 days ago by
manaswiniparija3
▴
10
Recent Votes
Recent Locations •
All
United States, just now
Norway, just now
United States, 3 minutes ago
Stony Brook University, NY, 4 minutes ago
South Korea, 4 minutes ago
European Union, 4 minutes ago
United States, 5 minutes ago
Recent Awards •
All
Popular Question to
lait
▴
170
Popular Question to
blur
▴
270
Popular Question to
Tawny
▴
180
Scholar to
rpolicastro
12k
Scholar to
Joel Wallenius
▴
130
Recent Replies
Comment: switching from illumination to NEB prep kits
by
GenoMax
129k
If you are simply replacing the library prep kit then it will be compatible with normal illumina libraries. If there is a different adapter…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
by
Zhichao
•
0
yes, I have activated this conda environment. And the conda is in `PATH` .
At first, I create a new conda environment `conda create -n ne…
Comment: Limma returned only positive logFC values
by
ATpoint
72k
Raw counts, raw meaning not manipulated by any transformation. See limma and edgeR manual, it clearly covers that for using limma-trend and…
Comment: Alternative To interactions comparison in limma in DESeq2
by
ATpoint
72k
https://support.bioconductor.org/p/9143932/ -- see the lower parts where Michael Love answers, it comes down to numeric contrasts.
Comment: Limma returned only positive logFC values
by
melissachua90
▴
40
The `mat` is log2-normalized raw data. Is it feasible? Or should I feed in counts?
Comment: DESeq2 for different design and normalized counts
by
ATpoint
72k
Nope, please read the manual of DESeq2, it clearly tells to use raw counts. What "normalized counts" do you have exactly? limma-trend might…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
by
ATpoint
72k
Did you activate your conda environment? Is conda in `PATH`? Please describe what you did.
Comment: Limma returned only positive logFC values
by
ATpoint
72k
Bottom line is, if you are using an intercept-free model (that is what `~0+...` is doing) then you have to use contrasts. In a "normal" mod…
Comment: Asking for feedback on a Python library for computing alignments
by
Alexander
▴
70
Thanks for sharing ! It seems there is a problem to install on Kaggle cloud (like a Colab): I tried several ways: https://www.kaggle.com/co…
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Darked89
4.4k
I am not sure what you gain by using hard masked genome for RNA-Seq mapping. There will be reads covering some introns. But if you mask rep…
Comment: Extract sequences from a fastq file by a list of IDs
by
mhpakdel96
•
0
Thanks a lot, it works
Comment: Differential protein expression analysis
by
dsull
★
4.2k
I don't have a tutorial but see this paper I co-authored:
https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00666
All of the upstream …
Comment: Differential protein expression analysis
by
Ribo
▴
40
Thank you!
Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values
by
melissachua90
▴
40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values
by
Gordon Smyth
★
6.1k
No, your code isn't correct. You are testing one group mean equal to zero instead of testing for differences between two groups. I wonder w…
Traffic: 2400 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