User: juara
juara • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- Canada
- Last seen:
- 6 days, 21 hours ago
- Joined:
- 5 years, 9 months ago
- Email:
- n**********@gmail.com
Posts by juara
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... Hi again,
so I found out that in the case of `method = "ssgsea`, there is a normalization step across samples and genesets. It can be turned off with `ssgsea.norm = FALSE` to get scores independent of samples and genesets. However, I still have the same normalization issue with `method = gsva`.
Th ...
written 4 weeks ago by
juara • 30
6
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159
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5 follow
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... Hello,
I have a log2 normalized TPM dataset that I would like to do pathway enrichment analysis. I thought GSVA and ssGSEA would output enrichment scores independent of sample set. However, when I subset my dataset and rerun GSVA, I get totally different set of scores. Do you have an idea what that ...
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... Hello all,
my question is relevant to https://www.biostars.org/p/383688/ . I still do not understand how `consensusmap()` assigns each sample to a cluster as shown in consensus track. Manual plotting of maximum values from `coef(res)` gives me the basis component and not consensus cluster.
Any com ...
written 5 weeks ago by
juara • 30
2
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2
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166
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2
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... Hello all,
I have patient data that are grouped based on a characteristic. I ran DESeq2 between the two groups following the tutorial. Everything seems fine but when I plot one of the top differentially regulated genes using `plotCounts()`, it seems the difference is driven by few outliers. Here is ...
written 3 months ago by
juara • 30
• updated
3 months ago by
jordi.planells • 380
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... Dear All,
my question is related to this post: https://www.biostars.org/p/275874/
I have a heterogeneous RNAseq dataset in TPMs from 66 samples and two sequencing batches (64 from one batch, 2 from the second batch). This dataset contains many disease types (categorical), sample types (categorical ...
written 3 months ago by
juara • 30
0
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... Hello
I have a rather naive question. I ran GATK4 mutect2 on my samples with the following flags:
--contamination-fraction-to-filter 0.0
--max-reads-per-alignment-start 0
The former is to disable downsampling process. So, theoretically I should be able to have equal values in t_depth column (to ...
written 2.6 years ago by
juara • 30
0
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1
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1.4k
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1
answers
... Thank you very much for your comment. this works like charm! :)
I am just wondering, whether there is a function in bcftools that I can merge FORMAT field data to INFO field with? ...
written 2.6 years ago by
juara • 30
0
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1
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1.4k
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1
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... Yes I tried that too. The bcftools comment works though! Thanks ...
written 2.6 years ago by
juara • 30
4
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1
answer
1.4k
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1
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... Hello
I have VCF outputs of Mutect2 (GATK4) with no downsampling. Some variants have multiple calls, which are comma separated in ALT column. I would like to preserve all of them before inputting in VEP including their respective TLOD and AF scores into a new VCF file where each alternative allele ...
written 2.6 years ago by
juara • 30
• updated
2.6 years ago by
Pierre Lindenbaum ♦ 134k
3
votes
0
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1.3k
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... Hello
I am interested in specific loci of the genome in TARGET WGS data and so am trying to download only those regions as opposed to the whole SRA files which takes forever to download. So far, I figured that I can download the SRA files, convert them to BAM, take a slice of interest and delete th ...
written 3.4 years ago by
juara • 30
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