User: piyushjo
piyushjo • 170
- Reputation:
- 170
- Status:
- Trusted
- Location:
- Last seen:
- an hour ago
- Joined:
- 1 year, 6 months ago
- Email:
- p*******@gmail.com
Posts by piyushjo
<prev
• 83 results •
page 1 of 9 •
next >
0
votes
1
answer
331
views
1
answers
... Did you PCA plot cells by there S, G2M and G1 score and saw different cluster for each stage like Fig 3 in tutorial? If yes, then it suggest that cell cycle genes have significant input to variation. If not then they don't, in that case regressing wouldn't make any difference. If you did see differe ...
written 6 weeks ago by
piyushjo • 170
0
votes
0
answers
155
views
0
answers
Comment:
C: HISAT2 index building
... I am not an expert but I did get an opinion from a person who provide core services at the NIH, that you need to be have the transcriptome GTF for building the index. Do it without the exon information and it will be fine. You will be using the annotation file while quantifying.
I am doing exactly ...
written 7 weeks ago by
piyushjo • 170
1
vote
1
answer
150
views
1
answers
... Any annotation, whether RefSeq or GENCODE already includes bunch of lncRNAs. You can use biomaRt package to figure out which of the gene id's belong to lncRNA class.
If you looking for novel lncRNAs, those that are not annotated yet, there are bunch of papers you can follow.
https://www.nature.c ...
written 8 weeks ago by
piyushjo • 170
0
votes
2
answers
1.8k
views
2
answers
... Use the biomaRt vignette. If you have ids as ensembl gene ids it is pretty easy. Let x be a character array with your ensembl gene ids (with and without version information)
goids = getBM(attributes = c('ensembl_gene_id', 'gene_biotype'),
filters = 'ensembl_gene_id',
...
written 9 weeks ago by
piyushjo • 170
0
votes
1
answer
233
views
1
answers
... Thanks for your insight! ...
written 9 weeks ago by
piyushjo • 170
0
votes
1
answer
233
views
1
answers
... Ok I understand your clarification, but what would you suggest doing when I really want to find something that connects the two sets that I know for sure are overall different. For example, if I have a differentiating neuronal culture from Day 1 and Day 2 and I am really interested in finding the tr ...
written 9 weeks ago by
piyushjo • 170
4
votes
1
answer
233
views
1
answer
... Hi,
So I have two datasets from two different yet related cell lines: pre and post relapse cancer cell line from same patient.
I have performed single cell sequencing for both of them with the hypothesis that I will be able to find rarely expressed cells in either that are key to becoming relapse. ...
written 9 weeks ago by
piyushjo • 170
• updated
9 weeks ago by
jared.andrews07 • 3.7k
0
votes
1
answer
331
views
1
answers
... Ok Thank you for your explanation. ...
written 9 weeks ago by
piyushjo • 170
2
votes
1
answer
331
views
1
answer
... Hi,
I am using cancer cell line scRNA-seq data to fing rarely expressed cells in homogenous cell culture. I am following seurat vignette for clustering. I also fund the seurat tutorial to regress out cell cycle genes effect.
However, I have a basic question. My current work is as follow:
1) Find v ...
0
votes
2
answers
175
views
2
answers
... Follow the example in the link below. It will help you get correlated gene cohorts and also do some trait relationships. There are also tutorials on the first link (ucla.edu), but I find the tutorial below much easier to understand.
https://wikis.utexas.edu/display/bioiteam/Clustering+using+WGCNA ...
written 11 weeks ago by
piyushjo • 170
Latest awards to piyushjo
Popular Question
10 weeks ago,
created a question with more than 1,000 views.
For How different is rlog transformation from vst transformation in DESeq2
Scholar
12 weeks ago,
created an answer that has been accepted.
For A: Get a bunch of ENTREZID into gene symbols
Popular Question
6 months ago,
created a question with more than 1,000 views.
For How different is rlog transformation from vst transformation in DESeq2
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1866 users visited in the last hour