updated 21 hours ago by
Ram
39k
•
written 3.5 years ago by
muhammad.khizerkiet
•
0
0
votes
8
replies
1.5k
views
0
votes
6
replies
329
views
2
votes
6
replies
646
views
0
votes
4
replies
652
views
0
votes
3
replies
218
views
updated 13 hours ago by
Ram
39k
•
written 19 hours ago by
Researcher
•
0
3
votes
3
replies
190
views
1
vote
3
replies
200
views
1
vote
3
replies
67
views
2
votes
3
replies
213
views
1
vote
3
replies
598
views
updated 19 hours ago by
Ram
39k
•
written 3.4 years ago by
Can Holyavkin
▴
240
0
votes
2
replies
21
views
2
votes
2
replies
182
views
0
votes
2
replies
770
views
0
votes
2
replies
224
views
0
votes
2
replies
186
views
14 hours ago by
mattze731
▴
10
0
votes
2
replies
141
views
0
votes
2
replies
301
views
23 hours ago by
zhangdengwei
▴
190
0
votes
1
reply
71
views
updated 6 hours ago by
seidel
11k
•
written 7 hours ago by
dare_devil
★
3.1k
0
votes
1
reply
98
views
0
votes
1
reply
10
views
0
votes
1
reply
127
views
updated 16 hours ago by
acvill
▴
290
•
written 23 hours ago by
tahsinkhan570
•
0
0
votes
1
reply
159
views
0
votes
1
reply
13
views
1
vote
0
replies
96
views
22 hours ago by
zhangdengwei
▴
190
0
votes
0
replies
7
views
0
votes
0
replies
480
views
updated 18 hours ago by
Ram
39k
•
written 3.5 years ago by
vafamayahi
•
0
0
votes
0
replies
588
views
0
votes
0
replies
26
views
2 hours ago by
Aanushka
•
0
0
votes
0
replies
11
views
0
votes
0
replies
15
views
0
votes
0
replies
368
views
updated 20 hours ago by
Ram
39k
•
written 19 months ago by
ezraamustafa3
•
0
0
votes
0
replies
12
views
47 minutes ago by
blur
▴
270
Recent Votes
Recent Locations •
All
Switzerland, just now
France, just now
Santiago de Compostela, Spain, 1 minute ago
United States, 1 minute ago
Germany, 3 minutes ago
Italy, 6 minutes ago
Finland, 6 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: 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…
Answer: Extract sequences from a fastq file by a list of IDs
by
GenoMax
129k
Using `filterbyname.sh` from [**BBMap suite**][1]:
You need to include the `/1` in the header in your list file (here I am using the `nam…
Traffic: 2243 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