User: Thind amarinder
Thind amarinder • 90
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Posts by Thind amarinder
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Comment:
C: Gene list from bed file
... I tried this and I would like to add something extra. Also select Track:- UCSC. I obtained multiple lines w.r.t. original co-ordinates in .bed so I collapsed it using bedtools: `bedtools map -a original.bed -b ucsc_based_gene_list.bed -c 5 -o collapse` ...
written 2 days ago by
Thind amarinder • 90
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... Where do we suppose to mention the version of the genome reference hg19/hg38 etc? ...
written 9 days ago by
Thind amarinder • 90
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... I see QLF has advantages over LRT, with some exceptions. [Mentioned by Aaron Lun here][1]..... where the dispersions are very large and the counts are very small, whereby some of the approximations in the QL framework seem to fail.
[1]: https://support.bioconductor.org/p/84291/#84292 ...
written 23 days ago by
Thind amarinder • 90
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... Is there any way to correlate VAF information with bulk-transcriptome expression after adjustment of purity and ploidy of the cancer samples? e.g., in one of the samples, I found that the VAF is 0.17, and the copy number of the samples is ~5 (after adjustment of purity and ploidy by the purple tool) ...
written 5 weeks ago by
Thind amarinder • 90
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... Thanks for your point. Do you think, a comparison of the [house-keeping][1] genes expression between GTEx and data I have, could give me some hints about the different present because of technical artifacts?
[1]: https://www.genomics-online.com/resources/16/5049/housekeeping-genes/ ...
written 6 weeks ago by
Thind amarinder • 90
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... I want to compare gene expression, in the way [Gepia tool][1] does by using log2(TPM) values. I have a condition which I would like to compare for a specific gene or set of genes with normal tissue expression (GTEx). I am thinking of comparing the log2(TPM+1) expression of normal tissue expression o ...
written 6 weeks ago by
Thind amarinder • 90
• updated
6 weeks ago by
ATpoint ♦ 40k
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... Thank you very much for the feedback. Yes, there were corrections on `PCAtools` related lines. After verification of estimateDisp from edgeR documents, I may include `FilterByExpr` function to edgeR related part and again I need to check what's the best way for deseq2 in that case. ...
written 6 weeks ago by
Thind amarinder • 90
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... @kevin Blighe In your PCAtools package. Do we need normalized count as an input or raw count and how variance is calculated? Do we need to perform rlog type transformation before performing the PCA? ...
written 9 weeks ago by
Thind amarinder • 90
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Answer:
A: PHYLIP to MEGA converter
... [https://www.biostars.org/p/173079/#454867][1]
I answered it here.
[1]: https://www.biostars.org/p/173079/#454867 ...
written 11 weeks ago by
Thind amarinder • 90
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... Using R, it is very simple, Here is my R script.
[https://github.com/amarinderthind/phlyip-distance-to-Mega-distance/blob/master/distane_matrix_conversion.r][1]
library(readr)
dist1 <- read_table2("input_file_phylip_distance.txt", col_names = FALSE, skip = 1)
names1 <- dist ...
written 11 weeks ago by
Thind amarinder • 90
Latest awards to Thind amarinder
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18 days ago,
created a post with more than 5 votes.
For RNASeq tutorial for gene differential expression analysis
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created a question with more than 1,000 views.
For Not able to retrieve PDB id from standalone blast against PDB
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voted at least 25 times.
Popular Question
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created a question with more than 1,000 views.
For Not able to retrieve PDB id from standalone blast against PDB
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