Moderator: igor

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igor8.1k
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Posts by igor

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Answer: A: How to know whether identified mutation signatures from my data are listed in CO
... 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 igor8.1k
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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 igor8.1k
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Comment: C: Library size normalization during CNV calling from genomically doubled tumor tis
... 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 igor8.1k
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Comment: C: Library size normalization during CNV calling from genomically doubled tumor tis
... Yes, they estimate ploidy, but it is based on allele frequencies, not library size. ...
written 10 days ago by igor8.1k
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Comment: C: Library size normalization during CNV calling from genomically doubled tumor tis
... 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 igor8.1k
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Comment: C: How to retrieve VCF of C. elegans and D. melanogaster
... There are species-specific SNP databases, such as BDGP: https://www.fruitfly.org/SNP/ ...
written 15 days ago by igor8.1k
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Answer: A: Why does every database have a different set of exons for TP53 (and other genes)
... 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 igor8.1k
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Comment: C: How to retrieve VCF of C. elegans and D. melanogaster
... dbSNP has other organisms (although they are no longer updated): ftp://ftp.ncbi.nih.gov/snp/organisms/archive/ ...
written 15 days ago by igor8.1k
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Comment: C: clusterprofiler GSEA function no term enriched under specific pvalueCutoff...
... Can you do `head(up.genes[[2]])` and `head(m_t2g)`? ...
written 16 days ago by igor8.1k
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Answer: A: What batch correction was applied to pan-Cancer mRNA expression data?
... 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 igor8.1k

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