User: hibernicah
hibernicah • 10
- Reputation:
- 10
- Status:
- New User
- Location:
- Last seen:
- 2 days, 21 hours ago
- Joined:
- 1 year, 5 months ago
- Email:
- h*********@gmail.com
Posts by hibernicah
<prev
• 8 results •
page 1 of 1 •
next >
0
votes
0
answers
87
views
0
answers
... Do you think that pseudogenes masking for short-reads mapping is sensible? I'm analysing ribosome profiling data that are about 25-32 nt long and even after standard pre-alignment to rRNA region I still see some multi mapping that maybe could be diminished if pseudogenes regions were hard-masked in ...
written 4 days ago by
hibernicah • 10
0
votes
1
answer
144
views
1
answers
... In order to narrow down a list of GO/pathways you can explore the pathways in terms of GO hierarchy as I mentioned earlier or simply adding more stringent threshold for significance, minimum or maximum number of genes in the pathway that was in an input list etc. ...
written 4 days ago by
hibernicah • 10
0
votes
0
answers
212
views
0
answers
... I'm using `GSEA` function to perform enrichment analysis on my pre-ranked gene list. The function takes only genes sorted in decreasing order by a metric of choice, so I've ordered genes by decreasing DESeq2 test statistics, which reflects direction and significance of change.
When I revert the or ...
written 9 weeks ago by
hibernicah • 10
0
votes
1
answer
144
views
1
answers
... What do you mean by further analysis? Do you see eg. stress response associated signatures enrichment and you want to summarise them for visualisation or do you want to draw more general conclusions from your data that you were unable to see so far? ...
written 9 weeks ago by
hibernicah • 10
1
vote
1
answer
144
views
1
answers
... Gene ontologies are organised into a hierarchical tree structure, which means that smaller gene sets are usually a subset of a larger, broader set that may be helpful to categorise your results. You can also explore annotated relationship between them, see: [http://geneontology.org/docs/ontology-rel ...
written 9 weeks ago by
hibernicah • 10
0
votes
0
answers
540
views
0
answers
... Yes I agree. The problem is that translation changes are highly correlated with transcript abundance and we don't know what is the "normal" translational response to changing mRNA abundance. The safe option seems to be define translationally regulated genes as genes that shows changes only in the Ri ...
written 14 months ago by
hibernicah • 10
0
votes
0
answers
540
views
0
answers
... Thank you for such a quick reply. This is a good point. Usually with a simple experiment design I do separate analyses for RNA-Seq and Ribo-Seq experiment, which in that case should look like this:
dds <- DESeqDataSetFromMatrix(counts, ~ cell_line + condition + time + condition:time)
dds ...
written 14 months ago by
hibernicah • 10
0
votes
0
answers
540
views
0
answers
... I am analysing the following experiment: two cell lines representing the same disease subtype were treated with a drug or DMSO (control) and the samples were collected in 4 time points: 0.5, 1, 6, and 16 h. Two types of sequencing were performed for each sample: Ribo-Seq to measure translatome and R ...
written 14 months ago by
hibernicah • 10
Latest awards to hibernicah
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1144 users visited in the last hour