User: cindy.perscheid

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90
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Location:
Hasso Plattner Institute, Potsdam, Germany
Website:
https://hpi.de/plattne...
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5 months ago
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1 year, 2 months ago
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Posts by cindy.perscheid

<prev • 19 results • page 1 of 2 • next >
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Comment: A: Master dictionary of database file (2D dictionary) using Biopython, then specify
... Well, if the desired information is always hidden inside these brackets and you can make sure that these are the only occurrences of those brackets, why don't you search for the occurrences of "[" and "]" to retrieve start and end index, and then get the corresponding substring of rec.description? ...
written 11 months ago by cindy.perscheid90
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Answer: A: gTEX normalize counts by genotype
... Hi, could you specify what you mean with "normalized by genotypes" here? As far as I understand, you have gene counts on the other hand, and a genotype (with variants, ergo non-numerical?) on the other hand. What would be your intention to do such a thing? Best, Cindy ...
written 11 months ago by cindy.perscheid90
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Comment: A: Master dictionary of database file (2D dictionary) using Biopython, then specify
... Hi, could you please specify your concrete question here (it seems there are a couple of them)? Besides, as your question is rather of a "programming" nature, I would recommend to search for your problem on Google and especially at Stackoverflow (kind of biostars for programmers). From my experie ...
written 11 months ago by cindy.perscheid90
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Answer: A: calculate RPKM from featureCounts result
... Hi yuabrahamliu, RPKM itself is the normalization function. ;) However, I would not recommend to use RPKM for your analysis, as it is considered to be not suitable anymore (see recent discussion [here][1] and publication comparing the different normalization strategies [here][2]). I would rather re ...
written 11 months ago by cindy.perscheid90
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Answer: A: Multiple TCGA expression datasets
... I used the TCGAbiolinks R package: https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html#gdcquery:_searching_tcga_open-access_data I implemented a python wrapper that creates an R script to generate an expression data set that is ready for downstream ML anal ...
written 11 months ago by cindy.perscheid90
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Answer: A: Multiple TCGA expression datasets
... As far as I know for the GDC, you can only query the data with parameters like study group, sample type, platform, and specific barcodes as the files are only available sample-wise (I suppose it is the same for all the other sources where you can download the data). I am afraid that you have to impl ...
written 11 months ago by cindy.perscheid90
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Comment: C: GDC TCGA Metadata no project ID available?
... Hi bharata, no, I have used TCGAbiolinks, who use the GDC API for querying. When downloading, they also get the metadata (the whole object is a SummarizedExperiment that contains both the expression counts and metadata) I can then access. Best, Cindy ...
written 12 months ago by cindy.perscheid90
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Data set with both genetic variants and gene expressions
... Hi there, as it seems getting access to the recently published GTEx data set (https://www.biorxiv.org/content/biorxiv/early/2016/09/09/074443.full.pdf; see discussion here https://www.biostars.org/p/283484/#283521) is quite hard for non-US institutions, I was wondering whether it is easier to just ...
gene expression causal relationship gtex variants written 12 months ago by cindy.perscheid90 • updated 9 months ago by Biostar ♦♦ 20
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Comment: A: GDC TCGA Metadata no project ID available?
... As it here is only about a couple of barcodes with missing project_id, as we can look up the assigned study of them, and as we have no idea why this happens - I would now just try to fix the issue by manually filling in the project_id. Any concerns with this? Best, Cindy ...
written 12 months ago by cindy.perscheid90
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Comment: C: Experience with dbGaP controlled access from outside the US?
... Thanks for the hint. It turns out we already have a DUNS number, so I will probably give it a try. When I read about all the other web pages for registration and always just saw "US government" and "grants" I had the impression that it is not possible for non-US-granted institutions at all. Good to ...
written 12 months ago by cindy.perscheid90

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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: calculate RPKM from featureCounts result

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