User: Minstein

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Minstein70
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Posts by Minstein

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Answer: A: Where can I find public Single Cell RNA-seq data?
... More than 20 human and mouse scRNA-seq datasets are collected by the [Hemberg Group][1]: https://hemberg-lab.github.io/scRNA.seq.datasets/ [1]: https://www.sanger.ac.uk/science/groups/hemberg-group ...
written 4 weeks ago by Minstein70
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Answer: A: why PCA for RNA-Seq but tSNE for scRNA-seq?
... I think tSNE is capturing **the local relationships** between points, like treating your data as a network where your cells are nodes. PCA is calculating **the "true" distances** between points after we consider **variation in your dataset**. Mahalanobis distance can do similar things. Applying PCA ...
written 4 months ago by Minstein70
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Answer: A: Unsupervised subtype discovery
... I'd say you'd better filter out some genes, because if some genes don't contribute to the subtype identification, they may add noises to your data. The assumption behind is that there should be some common features among different subtypes, but due to the measurement, there are variations in the com ...
written 4 months ago by Minstein70
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(Closed) [R/Rstudio] Can't load installed packages with "no title available" message
... I installed Rstudio in our lab's server, and run as a non-root user. I usually installed R packages in a directory created by my self and I have the privilege to read and write. However, I found packages installed previously in that directory can no longer be used, and there are error messages which ...
software error R written 4 months ago by Minstein70
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Answer: A: Merging single-cell RNA-seq from different platforms across different conditions
... Hi, Marta Two papers published this year in Nature Biotechnology solved the problem of batch effect correction between scRNA datasets: 1. Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. (https://www.nature.com/articles/nbt.4091) 2. Integratin ...
written 4 months ago by Minstein70
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Comment: C: Why NMF for mutation signature analysis
... Thanks. It makes sense now. ...
written 4 months ago by Minstein70
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Comment: C: Why NMF for mutation signature analysis
... My thinking is: Sparsity can help you interpret the biological meaning for the ***metagenes***, because only a few numbers of coefficients are positive and it helps you better understand the function of that group of genes. You can think of the expression profile or mutation profile as the output of ...
written 4 months ago by Minstein70
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Answer: A: Why NMF for mutation signature analysis
... The mutational profile is naturally nonnegative. You can regard the latent k components as a combination of genes (i.e. metagene). NMF can help you see which "parts" of genes function in which class of patients. In the case of face recognition, NMF can help you identify intuitional parts of faces, ...
written 4 months ago by Minstein70
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How to predict protein domains from a list of mRNA sequences?
... I have a list of mRNA (mature mRNA) sequences. I performed the transcriptome assembly, so some of the mRNA sequences have not been annotated before. My aim is to annotate domains for all the potential amino acid sequences from these mRNAs. Some obstacles exist: - A *de novo* protein domain predic ...
genome sequence written 4 months ago by Minstein70
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Answer: A: Conserved Domain Batch Retrieval
... You can try **Batch CD-Search** from NCBI: https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi. > Batch CD-Search serves as both a web application and a script > interface for a conserved domain search on multiple protein sequences, > accepting up to 4,000 proteins in a single job. I ...
written 4 months ago by Minstein70

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Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Why NMF for mutation signature analysis

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