User: Lila M

gravatar for Lila M
Lila M 900
Reputation:
900
Status:
Trusted
Location:
UK
Last seen:
11 hours ago
Joined:
5 years, 4 months ago
Email:
p*************@gmail.com

Posts by Lila M

<prev • 346 results • page 1 of 35 • next >
0
votes
0
answers
95
views
0
answers
What is the best approach to correlate expression levels, mutated genes and clinical variables
... Hi there, I was wondering which could be the best approach to correlate expression levels (from RNA -seq) mutated genes and clinical variables for a specific patients data set. I have two data frames, let's call them `exp` with the typical RNA-seq data processed by `DESeq2` and other table with g ...
correlation mutation rna-seq written 21 hours ago by Lila M 900
0
votes
0
answers
50
views
0
answers
Comment: C: best way to analyze a subset of DE genes
... because there is no other kind of analysis than can be done with the RNA seq apart from DE to test this kind of differences, right? ...
written 5 days ago by Lila M 900
0
votes
0
answers
50
views
0
answers
Comment: C: best way to analyze a subset of DE genes
... It is an in-house method who is very reliable actually (can't explain so far). It has not be tested as DE in lab, but the genes have an effect ...
written 5 days ago by Lila M 900
0
votes
0
answers
50
views
0
answers
best way to analyze a subset of DE genes
... Hi all, I have the RNAseq data for an experiment, with data under two condition. I've performed the typical DE analysis using `DESeq` in `R`. On the other hand, I have a positive control genes from the lab, but unfortunately, those genes are not DE in my analysis. So now, I'm wondering if there is ...
gene expression deseq rna-seq written 5 days ago by Lila M 900
1
vote
0
answers
65
views
0
answers
Comment: C: LEfSe for multiple samples
... you can try [this][1]. Other option is to use [Galaxy][2] m that has a very good implemented interface to address this issue. Is less manipulative but is very straight forward [1]: https://rdrr.io/github/ying14/yingtools2/man/lefse.html [2]: https://huttenhower.sph.harvard.edu/galaxy/ ...
written 5 days ago by Lila M 900
1
vote
0
answers
65
views
0
answers
Comment: C: LEfSe for multiple samples
... You can use `lefser` for that propose. Have a look into the argument `one.against.one : for multiclass tasks, sets whether testing is performed one-against-one (TRUE - more strict) or one-against-all (FALSE - less strict)` So if you have 5 groups: A,B,C,D and E, for the `all-against-all` featu ...
written 6 days ago by Lila M 900
0
votes
1
answer
148
views
1
answers
Comment: C: problem when create an expression matrix using a table
... yes but I get the same result :( ...
written 4 weeks ago by Lila M 900
0
votes
1
answer
148
views
1
answers
Comment: C: problem when create an expression matrix using a table
... my bad, the original table is `xx` and `mat` is the matrix that I can't get ...
written 4 weeks ago by Lila M 900
0
votes
1
answer
148
views
1
answers
Comment: C: problem when create an expression matrix using a table
... No, there is not a duplication for every gene ...
written 4 weeks ago by Lila M 900
0
votes
1
answer
148
views
1
answers
Comment: C: problem when create an expression matrix using a table
... It creates an empty table ...
written 4 weeks ago by Lila M 900

Latest awards to Lila M

Great Question 21 days ago, created a question with more than 5,000 views. For How to convert bedgraph to bigwig?
Popular Question 21 days ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 28 days ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 11 weeks ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 3 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 13 months ago, created a question with more than 1,000 views. For how to identify TATA box in a gene list
Epic Question 13 months ago, created a question with more than 10,000 views. For How to convert bedgraph to bigwig?
Popular Question 13 months ago, created a question with more than 1,000 views. For How to convert references ID list in UCSC reference list
Popular Question 13 months ago, created a question with more than 1,000 views. For How to convert bedgraph to bigwig?
Popular Question 13 months ago, created a question with more than 1,000 views. For how to set a proper d parameter in MACS
Epic Question 13 months ago, created a question with more than 10,000 views. For should I merge fastq files for different lanes before do QC?
Popular Question 13 months ago, created a question with more than 1,000 views. For Looking for a ClueGO (cytoscape) tutorial
Great Question 13 months ago, created a question with more than 5,000 views. For How to convert bedgraph to bigwig?
Popular Question 13 months ago, created a question with more than 1,000 views. For How can I check the direction of DNA replication?
Popular Question 13 months ago, created a question with more than 1,000 views. For Is possible to convert BSgenome object to GRange?
Popular Question 13 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Appreciated 17 months ago, created a post with more than 5 votes. For should I merge fastq files for different lanes before do QC?
Popular Question 17 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 17 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 19 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 19 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: error while reading bigwig files in computeMatrix (deeptools)
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: error while reading bigwig files in computeMatrix (deeptools)
Popular Question 21 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Great Question 23 months ago, created a question with more than 5,000 views. For How to convert bedgraph to bigwig?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1989 users visited in the last hour
_