User: TriS
TriS • 4.3k
- Reputation:
- 4,270
- Status:
- Trusted
- Location:
- United States, Buffalo
- Last seen:
- 1 day, 3 hours ago
- Joined:
- 6 years, 4 months ago
- Email:
- s*******@gmail.com
Posts by TriS
<prev
• 337 results •
page 1 of 34 •
next >
0
votes
1
answer
894
views
1
answers
... part of the answer can be found here for Seurat:
https://www.biostars.org/p/409790/
for Scanpy's code (https://github.com/theislab/scanpy/blob/master/scanpy/tools/_rank_genes_groups.py):
method
The default method is `'t-test'`,
`'t-test_overestim_var'` overestimates variance of ...
written 5 months ago by
TriS • 4.3k
0
votes
2
answers
1.0k
views
2
answers
... if those are the column names then you must have some sort of genes as row names. you gotta do a little bit of coding to define what genes belong to what cluster.
1- based on the cluster p.value and Log2FC define what belongs to what cluster
2- repeat that for all 20 clusters
3- color each gene base ...
written 13 months ago by
TriS • 4.3k
2
votes
2
answers
1.0k
views
2
answers
... or if you want to put them all together you can just color each group differently.
library(ggplot2)
ggplot(macrphage_list, aes(x = untreated.Log2.Fold.Change, y = -log10(untreated.P.Value), fill = myClusters)) + geom_point(size = 3) + geom_hline(yinterecept=-log10(10e-5)) + geom_vline(xi ...
written 13 months ago by
TriS • 4.3k
0
votes
1
answer
65k
views
1
answers
... this post is now pretty old, the data on cbioportal have been updated. that's why you see a difference ...
written 13 months ago by
TriS • 4.3k
0
votes
1
answer
65k
views
1
answers
... see comments above where I addressed this question ...
written 21 months ago by
TriS • 4.3k
0
votes
1
answer
65k
views
1
answers
... it's good practice to remove genes that have expression = 0 or very low expression in most samples. the % is up to you, this is an example, and I used 50% ...
written 21 months ago by
TriS • 4.3k
0
votes
1
answer
65k
views
1
answers
... that's because you are trying to assign a variable starting with the square bracket, which in R is used to subset variables. I'd suggest to get familiar with R first, instead of copy-paste the code above. that will help you preventing lethal mistakes
...
written 21 months ago by
TriS • 4.3k
0
votes
1
answer
65k
views
1
answers
... that will require quite a lil bit of coding, I'd suggest you to refine your question first and then contact a bioinformatician/statistician to help you coding it ...
written 21 months ago by
TriS • 4.3k
0
votes
1
answer
65k
views
1
answers
... you have to select patients based on the expression of two genes.
- choose your two genes
- classify patients based on the expression of both (i.e. `tp53 > 2 & pi3k > 2`)
- that will be your altered class
- the rest is not altered.
or you can also count patients that are altered for one an ...
written 21 months ago by
TriS • 4.3k
2
votes
1
answer
65k
views
1
answers
... this code is a guideline, not a copy and paste document. I'd suggest you to read a bit more about basic R usage and survival analysis before digging into this. it'll be time well spent ...
written 3.0 years ago by
TriS • 4.3k
Latest awards to TriS
Great Question
5 weeks ago,
created a question with more than 5,000 views.
For retrieve full TCGA datasets from cBioportal with R
Great Question
5 weeks ago,
created a question with more than 5,000 views.
For Plot average methylation levels across TSS region
Epic Question
5 months ago,
created a question with more than 10,000 views.
For retrieve full TCGA datasets from cBioportal with R
Great Question
11 months ago,
created a question with more than 5,000 views.
For Plot average methylation levels across TSS region
Popular Question
13 months ago,
created a question with more than 1,000 views.
For artifact/false peaks visible in wiggle files
Scholar
14 months ago,
created an answer that has been accepted.
For C: limma results topTable vs toptable differ
Scholar
21 months ago,
created an answer that has been accepted.
For C: limma results topTable vs toptable differ
Scholar
21 months ago,
created an answer that has been accepted.
For A: How to split gene names in my list?
Good Answer
2.1 years ago,
created an answer that was upvoted at least 5 times.
For A: How to check whether two genomic regions contact in 3D?
Great Question
2.1 years ago,
created a question with more than 5,000 views.
For retrieve full TCGA datasets from cBioportal with R
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For artifact/false peaks visible in wiggle files
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For breakdancer - cfg creation and chi square problem
Appreciated
2.4 years ago,
created a post with more than 5 votes.
For A: How to check whether two genomic regions contact in 3D?
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For indel position in repetitive regions
Appreciated
2.5 years ago,
created a post with more than 5 votes.
For A: How to check whether two genomic regions contact in 3D?
Popular Question
2.5 years ago,
created a question with more than 1,000 views.
For breakdancer - cfg creation and chi square problem
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For breakdancer - cfg creation and chi square problem
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For breakdancer - cfg creation and chi square problem
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For breakdancer - cfg creation and chi square problem
Popular Question
3.0 years ago,
created a question with more than 1,000 views.
For filtering pileup file with samtools for SomaticSniper
Scholar
3.2 years ago,
created an answer that has been accepted.
For C: limma results topTable vs toptable differ
Teacher
3.3 years ago,
created an answer with at least 3 up-votes.
For A: How to split gene names in my list?
Teacher
3.4 years ago,
created an answer with at least 3 up-votes.
For A: How to split gene names in my list?
Scholar
3.4 years ago,
created an answer that has been accepted.
For C: limma results topTable vs toptable differ
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1070 users visited in the last hour