User: nikitavlassenko

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Posts by nikitavlassenko

<prev • 23 results • page 1 of 3 • next >
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Answer: A: Common Gene Expression Pattern From Matrix
... Ultimately I decided to subdivide the dataset into certain groups, and use `FindMarkers` function to do `DE`: https://satijalab.org/seurat/de_vignette.html ...
written 10 weeks ago by nikitavlassenko0
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Common Gene Expression Pattern From Matrix
... I am using `Seurat` for my single cell `RNA-seq` dataset and I subset it to get a dataset of `80` cells vs `20 000` genes. Now I need to find genes that are expressed similarly across all of the `80` cells, similar patterns of expression. Can I do it with `Seurat`? What other software could I use fo ...
R rna-seq written 10 weeks ago by nikitavlassenko0
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Sample outlier detection in DESeq2
... I have 16 samples of bulk-RNA-seq data. There are 4 groups, so 4 samples are in each group. I want to check for outliers in each of the groups, and also get some characteristic estimate for each sample in each group of how much of an outlier it is. I am using `DESeq2`. There are threads that I found ...
deseq2 rna-seq written 12 weeks ago by nikitavlassenko0 • updated 12 weeks ago by genomax51k
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Comment: C: API for cells gene expression levels
... Yeah, ok, I mean gene symbols. Will see then. I just do not need anything (ensembl id, entrez id, whatever) but gene symbols. ...
written 3 months ago by nikitavlassenko0
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Comment: C: API for cells gene expression levels
... Ok, I tried out `EBI` and I suppose I can use `TPM` values in my app. However, there are no `mgi_symbols` in the matrix returned, for instance: ftp://ftp.ebi.ac.uk/pub/databases/arrayexpress/data/atlas/rnaseq/studies/arrayexpress/E-GEOD-39230/solanum_tuberosum/genes.tpm.htseq2.tsv So, do I need then ...
written 3 months ago by nikitavlassenko0
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Comment: C: API for cells gene expression levels
... Actually no, but I added the link to the `10X` question ...
written 3 months ago by nikitavlassenko0
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Comment: C: API for cells gene expression levels
... Yes, the question was linked, if I am not mistaken, to the one I also asked on `stackexchange`: https://bioinformatics.stackexchange.com/questions/4024/10x-illumina-demultiplexing-sample-sheet-issue/4046#4046 ...
written 3 months ago by nikitavlassenko0
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API for cells gene expression levels
... I am developing an iOS app to show various data about any cell's type (currently immune cells), and need to find somewhere an API that would let me query a genome database to retrieve gene expression values mainly (but further down the road other data too). I know that there is an 'ImmGen' app on 'A ...
genome database ios written 3 months ago by nikitavlassenko0
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Comment: C: bcl2fastq: Could not parse the CSV stream text
... Sure, their sample test works perfect ...
written 3 months ago by nikitavlassenko0
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Comment: C: bcl2fastq: Could not parse the CSV stream text
... I changed it to two read, not working. Removing all the top thing until `[Data]` gives sample sheet formatting error. Everything looks good in sample sheet, so either I need to somehow find what is actually wrong in samplesheet, some kind of a parsing, verifying program that would tell which line is ...
written 3 months ago by nikitavlassenko0

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