User: newbio17

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newbio1780
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Posts by newbio17

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Comment: C: Can one use Venn diagrams for identifying genes that are commonly differentially
... I'm not sure what the best way would be to properly generate set C. Treatment may be the same, but tissue and brain controls each may display different patterns of gene expression and different response to the treatment. Given the complications, authors seem to have performed differential expression ...
written 18 days ago by newbio1780
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Comment: C: selecting a transcript for in vivo validation
... I'm not sure what your data looks like, but if you're using RNA-Seq data to quantify transcript levels, maybe [tximport][1] is something you can use. [1]: http://bioconductor.org/packages/release/bioc/html/tximport.html ...
written 20 days ago by newbio1780
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Answer: A: Looking for dbSNP b144 version vcf
... It seems like you need to sift through the directories to get to the older versions. Below link should have all you need: [ftp://ftp.ncbi.nih.gov/snp/organisms/archive/human_9606_b144_GRCh37p13/VCF/][1] [1]: ftp://ftp.ncbi.nih.gov/snp/organisms/archive/human_9606_b144_GRCh37p13/VCF/ ...
written 21 days ago by newbio1780
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Comment: C: chromosomal distribution with sequence data
... If you're referring to distribution of reads across specific regions (i.e. coverage/depth) in a BAM file, you can try [mosdepth][1]. To locate genes on a chromosome, you can use the genomic coordinates in the [.gff][2] file you have. [1]: https://github.com/brentp/mosdepth [2]: https://www.n ...
written 21 days ago by newbio1780
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Answer: A: Download TCGA Published data
... Have you tried their legacy repository? [GDC Legacy Repository][1] You may want to play around with the filters, but it seems like they have BAM files you can download (restricted access). [1]: https://portal.gdc.cancer.gov/legacy-archive/search/f?filters=%7B%22op%22:%22and%22,%22content%22:%5B ...
written 21 days ago by newbio1780
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Answer: A: Somatic variant calling mutect2 tumour only
... As benformatics explained, tumor-only variant calling is not recommended and should be avoided if possible. With that said, GDC sometimes receive only tumor samples and have prepared PON, which is available on their page (scroll to bottom), to process the samples upon submitter's request: [GDC refe ...
written 5 weeks ago by newbio1780
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Comment: C: Using linear regression to accounting for confounding variables in gene expressi
... To clarify, I'm attempting to replicate the correlation analysis that was done in the paper below: https://www.biorxiv.org/content/biorxiv/early/2018/09/20/422592.full.pdf One of the steps that they perform is adjusting the expression levels of all samples according to tumor purity using linear reg ...
written 13 months ago by newbio1780
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Using linear regression to accounting for confounding variables in gene expression data
... My data consists of 20,000 rows (genes) and 300 columns (samples). 5 out of 300 are cell lines and 295 out of 300 are tumor samples. I'm currently attempting to adjust the expression values according to a confounding variable using linear regression. In summary, I have a dataframe consisting of the ...
linear regression rna-seq written 13 months ago by newbio1780 • updated 13 months ago by Charles Warden7.6k
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Comment: C: Correlation analysis between gene expression & tumor purity
... Thank you. Your posts are always helpful. ...
written 13 months ago by newbio1780
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Correlation analysis between gene expression & tumor purity
... What I have seen previously in papers is that the authors find genes that are highly correlated with tumor purity. - [Paper #1][1] - [Paper #2][2] I'm mainly confused in Paper #1, when author says: > "Spearman correlations were calculated between their expression and tumor purity to generate ...
correlation gene expression tumor purity rna-seq written 13 months ago by newbio1780 • updated 13 months ago by Devon Ryan94k

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Scholar 21 days ago, created an answer that has been accepted. For A: Looking for dbSNP b144 version vcf
Scholar 21 days ago, created an answer that has been accepted. For A: Looking for dbSNP b144 version vcf

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