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Gene ontology and homologs
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Recent Replies
Comment: TaxID mapping file
by
Lada
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30
if I understood correctly, I might need fle `prot.accession2taxid.gz` file? According to the [documentation][1] in column 2 is Accession.ve…
Answer: install package
by
Pine
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10
To follow on Mathew's reply, one way might be to try and see if you can download and install the package tarball locally:
1. Get the packag…
Answer: install package
by
Mathew
▴
50
Hi,
This is what happens when I run some code to diagnose the issue. First, I wanted to see what version of R was required for the package…
Answer: LD-prune variants while maintaining a list of SNPs
by
Jautis
▴
540
I was given a solution by a colleague -- it seems a little hacky, but worked really well!
> one way to get this to work is to use --clu…
Answer: Association study using SNP data
by
drajangirija
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0
Hi Matthew, Thank you very much for your inputs. I am working with Neogen genotyping data, which includes GC values less than 0.15.
Comment: Downloading full alignments from Pfam
by
bef1
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0
I tried contacting Pfam, they replied that indeed there is an issue on their side with the full alignments, which should be repaired in the…
Comment: Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Expe
by
Mensur Dlakic
★
27k
Don't know about others, but I would never contact someone about potential employment based only on their interests and with zero knowledge…
Comment: The GDC Legacy Archive is retiring soon.
by
Zhenyu Zhang
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1.2k
If you are talking about methylation idat files, they were all migrated from legacy to the data portal.
If you are talking about other pl…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Zhenyu Zhang
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1.2k
These TCGA samples were taken 10 ~ 20 years ago, and there is no way they have been treated by the modern immunotherapy.
Are you sure tha…
Comment: Design matrix Differential expression analysis
by
Gordon Smyth
★
7.1k
> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1))
It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
by
lorena9132
▴
10
Hi Mathew,
The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
by
Mathew
▴
50
Hi,
I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Answer: Association study using SNP data
by
Mathew
▴
50
Hi,
You asked three questions so I will attempt to help the best I can
**What should be the optimal GC score cutoff**
It sounds li…
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