Moderator: igor
igor ♦ 8.1k
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Posts by igor
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... There are packages available specifically for that purpose, such as [MutationalPatterns][1] or [deconstructSigs][2].
[1]: https://bioconductor.org/packages/release/bioc/html/MutationalPatterns.html
[2]: https://cran.r-project.org/package=deconstructSigs ...
written 3 days ago by
igor ♦ 8.1k
0
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1
answer
94
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Comment:
C: Analyzing VCF file
... There are a few suggestions here: https://www.biostars.org/p/363250/ ...
written 8 days ago by
igor ♦ 8.1k
0
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1
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140
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... I just wanted to clarify that library size is not used, which is what the original question was interested in. I was not disagreeing with anything that was stated. ...
written 10 days ago by
igor ♦ 8.1k
0
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1
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140
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... Yes, they estimate ploidy, but it is based on allele frequencies, not library size. ...
written 10 days ago by
igor ♦ 8.1k
0
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1
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140
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1
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... The library preparation and quantification that determines the library size is normally done based on the amount of DNA, not the number of cells. ...
written 10 days ago by
igor ♦ 8.1k
0
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0
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110
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... There are species-specific SNP databases, such as BDGP: https://www.fruitfly.org/SNP/
...
written 15 days ago by
igor ♦ 8.1k
1
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3
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158
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3
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... TP53 has multiple transcripts or splice variants. You can visualize that info in [Ensembl][1], for example. Each one has multiple exons and those may not be identical across every transcript.
What you are probably really looking for is the canonical transcript, but that's not an easy question to an ...
written 15 days ago by
igor ♦ 8.1k
2
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0
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110
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0
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... dbSNP has other organisms (although they are no longer updated): ftp://ftp.ncbi.nih.gov/snp/organisms/archive/ ...
written 15 days ago by
igor ♦ 8.1k
0
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answers
151
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0
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... Can you do `head(up.genes[[2]])` and `head(m_t2g)`? ...
written 16 days ago by
igor ♦ 8.1k
0
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2
answers
498
views
2
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... There is an explanation of `EB++AdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv` (should be the same as `EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv`) on [TCGA PancanAtlas Synapse][1]:
> File: EB++AdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv
>
> Contains batch normalized ...
written 22 days ago by
igor ♦ 8.1k
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