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Recent Replies
Comment: CNVKIT import errors
by
GenoMax
120k
Please use `conda` to do the installation. A basic tutorial is available here to use `conda` (use the part for `conda`): https://www.biosta…
Comment: CNVKIT import errors
by
ptoru001
•
0
hi all i am having similar errors with installation of cnvkit (for mac)...and cannot seem to figure it out...would anyone kindly please hel…
Comment: Ensembl Homology REST requests - possible to download whole database and query l
by
Pierre Lindenbaum
149k
>possible to download whole database and query locally?
http://ftp.ensembl.org/pub/current_compara/
Comment: High number of unmapped reads in STAR
by
Negara
•
0
I have added a link in my original post to the genome files I am using. These are human samples (paired end reads). I wonder why this much …
Answer: Convert Gene Ensemble IDs to Gene Symbols on R
by
ngarber
▴
50
The biomaRt package is the best way to do it, I believe, although I personally am using an equivalent package in Python. However, the princ…
Comment: Batch effect correction with cell type enrichment analysis
by
ATpoint
65k
Not very difficult, it’s impossible.
Comment: Should assemblies be removed if core gene alignment is identical?
by
c_u
▴
480
That was very helpful. Thank you so much!
Comment: Creating dominant and recessive models for burden test
by
LChart
840
They link to their software in the paper, no?
https://bitbucket.org/Wenan/cocorv/src/master/
Comment: Is there a setting in GSEA software to filter counts less than 10 before go for
by
LChart
840
Which GSEA software, specifically?
Comment: Batch effect correction with cell type enrichment analysis
by
LChart
840
> The reason I'm applying batch effect is that I have two sources, and I don't want any variation that is not biological.
Based on your de…
Comment: Detection of O6 Guanine methylation levels
by
Guruprasadh
▴
10
Dear Matthias,
Thanks for the inputs! Yes a good suggestion indeed. Thanks
Comment: Convert Gene Ensemble IDs to Gene Symbols on R
by
Marco Pannone
▴
480
I do not know why you are mentioning normalization now since it has nothing to do with the ID of a transcript in your dataset. However, I g…
Comment: Detection of O6 Guanine methylation levels
by
Matthias Zepper
1.7k
Might be worth talking to Oxford Nanopore? I know that they can already detect 5mC, 5hmC, 6mA, and BrdU in DNA and m6A in RNA and might be …
Comment: Convert Gene Ensemble IDs to Gene Symbols on R
by
Amr
▴
80
But how I can see their symbols in the unnormalized data? How their symbols have been obtained?
Comment: Convert Gene Ensemble IDs to Gene Symbols on R
by
Marco Pannone
▴
480
So naturally, you are not going to see them associated with any "Gene Symbol" when doing the conversion from "Ensembl ID".
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