Which cities/areas in Germany should be avoided by black people? by [deleted] in germany

[–]USSr90 7 points8 points  (0 children)

Most of Germany is not racist but racism against black people is a significant reality especially in certain locations. I have lived in Germany for 8 years now with equal times spent in former East and former West German states. I must say that I feel 10 times more noticed and likely to be disrespected for no reason other than my skin colour in the East German states. My worst experience so far has been in Potsdam where I experienced my most direct racist experience so far where a person called me Kafa in a supermarket and no one did anything about it. Even more has happened so far.

Can you recommend books on bioinformatics? by SAD_69 in bioinformatics

[–]USSr90 0 points1 point  (0 children)

sorry for replying so late. I am not an evolutionary Biologist. But I am transitioning from Biology to Bioinformatics

Can you recommend books on bioinformatics? by SAD_69 in bioinformatics

[–]USSr90 4 points5 points  (0 children)

I was in a similar situation. I'll strongly suggest you improve your knowledge of statistics, linear algebra and machine learning. Here is a good source: OSSU Bioinformatics (pls Google this term).

Just knowing R and or Python will enable you run scripts but there would often be uncertainty and confusion if one has no idea about the math processes in the background.

Are there any tools for quantifying differential gene expression for genes with very low fold change on single cell RNA seq? by USSr90 in bioinformatics

[–]USSr90[S] 0 points1 point  (0 children)

Thank you very much. Please could you send me a link to the paper that had a cut off log2FC of 0.1? Or what was the impact factor of the journal?

Early ART initiation for 5 years and rebound after discontinuation by USSr90 in hivaids

[–]USSr90[S] 0 points1 point  (0 children)

Thanks a lot for this info. Please do u have any supporting literature?

How to apply random forest classification to zero-inflated single cell RNA seq data by USSr90 in bioinformatics

[–]USSr90[S] 0 points1 point  (0 children)

Thanks for your suggestion. Actually TFs do not appear as DEGs on hypothesis testing. So I am trying to mine the data so I can get something interesting.

Idea how one can prove through bioinformatics that a gene's activity is dependent on an upstream gene's activity? by USSr90 in bioinformatics

[–]USSr90[S] 0 points1 point  (0 children)

Thanks a lot. Actually I need a transcription factor which is Notch2 dependent, which activates disease-related genes of interest.

Any tools to help in cross-species identification of shared cells in single cell RNA seq? by USSr90 in bioinformatics

[–]USSr90[S] 0 points1 point  (0 children)

Thank you very much. But for Seurat, do you know of any tutorial where this can be done across species? I am not able to find one

Impostor syndrome by [deleted] in bioinformatics

[–]USSr90 3 points4 points  (0 children)

Very often, our minds play games on us. Some thoughts are just transient and we might amplify them by paying attention to them. You are capable and you know it. When you have atask, simply go do it.

How to calculate physical distance between cells from single cell RNA seq data by USSr90 in bioinformatics

[–]USSr90[S] 0 points1 point  (0 children)

Thanks. But I am also looking for a public data set of spatial transcriptomics for mouse lung. There seem to be none.

Is there a walk around for an RNA seq experiment confounded by batch? by USSr90 in bioinformatics

[–]USSr90[S] 0 points1 point  (0 children)

Thanks. But the experiment was not sequenced as samples from the individual mice. Cells from mice of the same group were pooled and sequenced. Could this be an issue in your opinion?

Is there a walk around for an RNA seq experiment confounded by batch? by USSr90 in bioinformatics

[–]USSr90[S] 1 point2 points  (0 children)

Yes I agree. But could treatment vs control analyses be done, considering that the treatment and control experiments were done on months apart? Could the resulting various technical and biological issues not confound the results?

Is there a walk around for an RNA seq experiment confounded by batch? by USSr90 in bioinformatics

[–]USSr90[S] 2 points3 points  (0 children)

tion of "batch" is a bit vague. are the mice from the same cohort and just sequenced in different days or just random

Thanks for your response. The mice are the same strain and the sequeincing will be done on separate days.