User: popantrop

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popantrop50
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Posts by popantrop

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Job: Head of Bioinformatics at Biomage
... We are an early-stage startup building a data analytics tool for single-cell RNA-seq. Following our recent successes, including delivery of a pilot of the platform to Harvard Medical School and raising a seed round we are hiring for a position of senior bioinformatician (head of bioinformatics). Pl ...
single-cell rna-seq job rna-seq written 12 weeks ago by popantrop50
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Comment: C: How do genotype likelihoods (PL) work in gVCF files?
... Thanks, that sounds like good advise! ...
written 19 months ago by popantrop50
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How do genotype likelihoods (PL) work in gVCF files?
... I ran GATK4 on a single WES BAM file from The Cancer Genome Atlas (TCGA) program. This is how an example SNP call looks like: chr22 10685693 . A G, 307.60 . BaseQRankSum=1.267;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.582;RAW_MQandDP=91525,52;ReadPosRankSum=0.279 GT:AD:DP: ...
vcf genotype snp written 19 months ago by popantrop50
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Comment: C: How does monocle identify the begging of pseudotime?
... Thank you Kristoffer -- this makes sense. I think it's a bit misleading of the authors to be speaking of the "beginning of pseudotime", which could just as well be the end of pseudotime. Yes, RNA velocity can establish precedence, as I've written at the bottom of my question. The way this is done is ...
written 2.0 years ago by popantrop50
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How does monocle identify the begging of pseudotime?
... [The following graph][1] shows an example cell trajectory analysis with monocle. I have a rough understanding of how monocle constructs the pseudotemporal ordering of cells, using independent component analysis and minimum spanning trees (MST). However, there is one bit of the larger picture, which ...
scrna-seq rna velocity cell trajectory rna-seq written 2.0 years ago by popantrop50 • updated 2.0 years ago by kristoffer.vittingseerup3.5k
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Answer: A: Annotation Of Affymetrix Human Exon St. 1.0
... Your specific problem was most likely the fact that at the "core" annotation level RMA produces a file annotated with transcription cluster IDs, and biomart only speaks probeset IDs. So using biomart you can't translate from transcription cluster IDs to gene names. I've produced a [csv file](https: ...
written 2.6 years ago by popantrop50
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Writing and loading expression sets to and from csv files.
... One can write an expression set into a csv file using `csv.write`. For example, using the standard [bladderbatch bioconductor package](https://bioconductor.org/packages/release/data/experiment/vignettes/bladderbatch/inst/doc/bladderbatch.pdf) the following code writes a csv file to the current worki ...
R bioconductor microarray written 3.2 years ago by popantrop50 • updated 3.2 years ago by Kevin Blighe69k
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Comment: C: Affymetrix Microarray Analysis In Python
... Actually, I've just checked and the code works also with python2 ...
written 4.2 years ago by popantrop50
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Answer: A: Affymetrix Microarray Analysis In Python
... [I have written a parser][1] in pure python 3, which can deal with Affymetrix CEL files, version 4. This version is difficult to parse, because it's binary and poorly documented. Data produced from Human Exon Chip should be compatible with this parser. If you're interested in parsing other versions ...
written 4.2 years ago by popantrop50

Latest awards to popantrop

Popular Question 17 months ago, created a question with more than 1,000 views. For How does monocle identify the begging of pseudotime?
Popular Question 22 months ago, created a question with more than 1,000 views. For Writing and loading expression sets to and from csv files.
Student 22 months ago, asked a question with at least 3 up-votes. For How does monocle identify the begging of pseudotime?

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