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Anand Rao
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andres.firrincieli
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Recent Replies
Answer: PTM-aware protein folding / docking
by
Mensur Dlakic
★
23k
Your assumption is correct - AlphaFold pTM has nothing to do with post-translational modifications. See [**here**][1].
Not to discourage…
Answer: Admixture cv error
by
Declan
•
0
I had this issue today and was able to resolve it by changing the random seed Admixture uses by adding `-s time` (which sets the random see…
Answer: Total No of Genes of GENCODE Release 43
by
ahmad
•
0
The following is the correct code
gtf_43<-rtracklayer::import('gencode.v43.primary_assembly.annotation.gtf')
dtgtf_43<-data.frame(gtf_4…
Comment: Total No of Genes of GENCODE Release 43
by
ahmad
•
0
Hello,
thanks for replying, by mistake I paste the wrong code. the following is the corrected
gtf_43<-rtracklayer::import('gencode.v43…
Comment: Kallisto bustools for scRNA-seq
by
dsull
★
4.0k
I have no idea what that is besides a bunch of jumbled sequences. You'll need look up the structure of the reads / library from wherever yo…
Comment: Aberrant splicing in bulk RNAseq
by
dsull
★
4.0k
First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
Comment: Using Copy Number Alterations detected in other studies for the same tumor cell
by
lethalfang
▴
90
There is some somatic SV study on these HCC1395: https://doi.org/10.1186/s13059-022-02816-6.
There is also a CNA preprint from years ago b…
Comment: Somatic truth set
by
lethalfang
▴
90
Just in case things are hard to find, for the WGS/WES, these are the data (what the file names mean: https://sites.google.com/view/seqc2/ho…
Comment: How to get subset of a Seurat object based on metadata?
by
jv
★
1.0k
Hmm, not sure why `subset` doesn't match to '0:CD8 T cell' but maybe it's the ":"?
An alternative option is the following:
```
idx <- whi…
Comment: GO enrichment analysis
by
Jeremy
▴
780
g:Profiler has an Arabidopsis option:
[g:Profiler][1]
[1]: https://biit.cs.ut.ee/gprofiler/gost
Answer: Any tips in landing a bioinformatic job?
by
Carambakaracho
★
3.2k
The first job is a nightmare and you will need some luck. I understand you're looking for an industry offering. Unfortunately I've worked o…
Comment: Best way to visualize .paf or .sam alignment to a fasta file
by
GenoMax
127k
Why not use IGV with SAM file?
If you want a text based viewer then ASCIIGenome: https://asciigenome.readthedocs.io/en/latest/
Answer: What is the NCBI's definition of an "atypical genome"?
by
MirianT_NCBI
▴
510
Hi,
You can find more information about what constitute an [atypical genome in this FAQ][1]. Here's the list of reasons for a genome to …
Comment: How to get subset of a Seurat object based on metadata?
by
sunyeping
▴
80
> skin$predicted_cell_type
Error in rep.int(x = colnames(x = x), times = length(x = i)) : unimplemented type 'NULL' in 'rep3…
Comment: using CITE-seq data to cluster single cells
by
chi.delta
▴
40
Let's say that based on known FACS data, I already know that three populations exist based on the two antibodies staining: single positive …
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