User: nikitavlassenko

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Posts by nikitavlassenko

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Comment: C: Differential gene analysis from a javascript based web app
... I need something like this: https://docs.microsoft.com/en-us/machine-learning-server/deployr/deployr-about But I do not want to use DeployR server itself, just need such an API. ...
written 3 days ago by nikitavlassenko10
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Comment: C: Differential gene analysis from a javascript based web app
... What about server-side javascript? I have `node.js` on the server. Maybe there are any other libraries in other languages that could be accessed easily from javascript? Like `C++`, idk... I actually think that `OpenCPU` is the right way to go, I am just not sure how to call it on the server from my ...
written 5 days ago by nikitavlassenko10
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Differential gene analysis from a javascript based web app
... I have two subsets of cells and their gene expression in a web app written in `javascript`. I need a way now to determine which genes are differentially expressed between the groups. I searched for `javascript` libraries but found nothing, so I reasoned to try using `OpenCPU` to call an `R script` l ...
R deseq2 javascript written 5 days ago by nikitavlassenko10
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Normalization method for single-cell RNAseq to be able to compare between datasets
... I need to find a normalization method (or a sequence of several algorithms applied, not only normalization) for single-cell RNAseq that would allow me to compare directly values between the experiments. There is a thread, but I think it deals with bulk-RNAseq: https://www.biostars.org/p/258550/ Th ...
python rna-seq R written 24 days ago by nikitavlassenko10
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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 4 months ago by nikitavlassenko10
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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 4 months ago by nikitavlassenko10
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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 5 months ago by nikitavlassenko10 • updated 5 months ago by genomax55k
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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 5 months ago by nikitavlassenko10
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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 5 months ago by nikitavlassenko10
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Comment: C: API for cells gene expression levels
... Actually no, but I added the link to the `10X` question ...
written 5 months ago by nikitavlassenko10

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Popular Question 23 days ago, created a question with more than 1,000 views. For Get gene symbols from gene ids for mouse using BioMart

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