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RogueBiochemist
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Recent Replies
Comment: Pheatmap x must be numeric
by
Kevin Blighe
86k
Please try `as.matrix(my_matrix)` or `data.matrix(my_matrix)`. Also, please ensure that the colnames of `my_matrix` are the same as the row…
Answer: rMats Run Does Not Generate More Than One Output Row Per File
by
Y
•
0
In case it was an issue with how I made the reference files for the experiments and controls I did the following (with paths removed due to…
Comment: MAKER: WARNING: Could not get initialization lock. Trying Again...
by
memy
▴
20
It is on a HPC cluster (SLURM-based) and MAKER is installed centrally from easybuild and configured with OpenMPI/4.1.4. I also installed it…
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
RogueBiochemist
•
0
In the end, changing `$sample` to `${sample//[$'\r\n']}` (i.e. replace any carriage return or newline characters with '') worked!
```
wh…
Comment: Automate the Splitting of a VCF File by Sample (bcftools)
by
RogueBiochemist
•
0
Thank you! Thankfully I found a really easy solution (forceful removal of the any control characters), but the help is greatly appreciated!
Comment: Automate the Splitting of a VCF File by Sample (bcftools)
by
RogueBiochemist
•
0
Thanks! To be fair, keeping -c1 shouldn't be a massive issue, because this only the first step in a pipeline that'll eliminate most of the …
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Tully
•
0
Thank you for your guidance, very useful! Thank you!
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Istvan Albert
98k
I would also say that the example I gave is just for fun to show what someone new to the field could get done right away after installing t…
Answer: Search RCSB with a list of protein names?
by
GenoMax
134k
Using [**EntrezDirect**][1] as noted to get structure accessions (output truncated to save space):
$ esearch -db structure -query TP53…
Answer: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Istvan Albert
98k
this appears to be a problem that comes from snpEff, all the other steps completed correctly
I'll have to check what is up with snpEff, bu…
Answer: Transfer harmony-integrated scRNA-seq data to scanpy
by
Radu Tanasa
▴
60
As you well noticed, harmony creates an embedding, it does not generate integrated normalized counts. If you need that, I suggest you use s…
Comment: How to convert data in r?
by
kalavattam
▴
180
I don't see the need for the `dplyr` library in this code. `c()`, `data.frame()`, `as.data.frame()`, `t()`, `apply()`, `unname()`, `unlist(…
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