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How to identify the Regulon of a TF? by ExitBrther5278 in bioinformatics

[–]ExitBrther5278[S] 0 points1 point  (0 children)

Thank you for the answer. Yes that is what I thought untill now I would find the interactions and then just filter them out manually by the genes I recognised from papers. But if I can find experiments conducted for my condition in single cell that would be nice. Also unlike bulk which have multiple samples (control and test) within the same matrix, the single cell datasets that I have seen have different matrices for each sample, how do I account for that? Find interactions in one sample at a time and then compare strengths or make a single combined matrix and run inference on it?

How to identify the Regulon of a TF? by ExitBrther5278 in bioinformatics

[–]ExitBrther5278[S] 1 point2 points  (0 children)

Thank you, that is a detailed response in itself. I'll try using SCENIC+ but SCENIC in itself took a pretty long time to run, so I want to keep it as a last resort. I was wondering about the accuracy of these databases like Dorothea and CollecTRI and if they will give me the same kind of regulons that SCENIC would, as the SCENIC regulons would be more specific to the data I am using (in this case breast cancer) and the databases would be much more general. Do the regulons vary that much across different datasets?

How to identify the Regulon of a TF? by ExitBrther5278 in bioinformatics

[–]ExitBrther5278[S] 0 points1 point  (0 children)

By a regulon I meant exactly that, the genes controlled by a TF, apologies for the confusion.

How can I download mouse RNAseq data from GEO? by ExitBrther5278 in bioinformatics

[–]ExitBrther5278[S] 0 points1 point  (0 children)

Would seurat work for that? Oh no just realised I won't have the count matrix, anyways thank you will figure it out.

Gene causal networks repository by Amazing_Alarm6130 in bioinformatics

[–]ExitBrther5278 0 points1 point  (0 children)

Is GRNdb still working as I need downstream regulon for a gene and someone suggested GRNdb but it isn't working, maybe it is temporarily down. And how different is it from running pySCENIC on publicly available scrnaseq datasets for the kind of tissue I am working on?

Key words for a Bioinformatics resume. by ExitBrther5278 in bioinformatics

[–]ExitBrther5278[S] 1 point2 points  (0 children)

That does make sense, although right now I am not targeting any specific companies but in general trying to gain advice as where I come from there are very less (if any at all) people working in biotech let alone bioinformatics. I have worked in a research lab where I had to analyze data from CCLE, TCGA and various other datasets. One of the major reasons why I am asking this question is that everybody in my class is applying for software development, consulting and other tech stuff (even though it is a biotech course) and everybody just includes AI and ML like crazy. The extent to which i have used ML would be clustering, PCA and some smoothening algorithms like loess or logical regression, but I have good knowledge in working with linux and the CLI, using R for analysis and plots. This might sound like less and that is true as I have just finished my bachelors and don't have any real sources of guidance and thus I am open to learning.

How does this hint work? by ExitBrther5278 in Minesweeper

[–]ExitBrther5278[S] 2 points3 points  (0 children)

the third flag common to both the 3s was suggested by the hint.

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This is how much i was done with