User: fracarb8

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fracarb870
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Posts by fracarb8

<prev • 20 results • page 1 of 2 • next >
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Comment: C: How to use FindSubCluster in Seurat?
... I have never used that function, so I could be completely off, but have a look at `FindMultiModalNeighbors`. It could be similar to `AddModuleScore`, which computes the score and add a column (score name) to your metadata. ...
written 2 days ago by fracarb870
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Answer: A: regressing out covariate from Seurat integrated data
... Why do you think it is not recommended? The sctransform_vignette clearly states that "we can also remove confounding sources of variation" . I wouldn't worry too much and I would run `SCTransform(myObject, vars.to.regress = "SampleID", verbose = TRUE)` (assuming SampleID is where your sample name ...
written 5 days ago by fracarb870
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Comment: C: Merge csv files with same columns and different rows in R
... Probably inefficient, but the quickest way I can think of would be to subset the 700 gene table so that it has the same genes as the 500 genes one, and merge the two together. Then rbind the merged table to the genes you discarded (200) . Wrap everything in a loop (or function) and you can merge al ...
written 14 days ago by fracarb870
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Comment: C: Is there other IDE like R studio working on the linux?
... BiocManager allows you to install "local" packages. You could download all the different version from bioconuctor and install them using different location (e.g setting different Rlibs) A quite convoluted way, but possible....I think. ...
written 24 days ago by fracarb870
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Answer: A: Is there other IDE like R studio working on the linux?
... The best way would be to install different versions of the same package in different libraries and switch between them as you need them > # read packages from library 1 > library(myPackage, lib.loc="~/Rlib/v1/myPackage") > # read packages from library 1 > library(myPackage, lib. ...
written 24 days ago by fracarb870
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Comment: C: Set.seed in Seurat
... you could `set.seed(42)` before running the commands, or you could put it at the beginning of the script. ...
written 3 months ago by fracarb870
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Answer: A: Set.seed in Seurat
... From the python implementation documentation: UMAP is a stochastic algorithm – it makes use of randomness both to speed up approximation steps, and to aid in solving hard optimization problems. This means that different runs of UMAP can produce different results. By setting the seed ...
written 3 months ago by fracarb870
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Comment: C: Cross-specie Integration Using Seurat
... check which assay you are using for the integration. I had a similar error once, when I was integrating "integrated" objects without setting the assay to "SCT" ( `DefaultAssay(object) <- "SCT"`). ...
written 4 months ago by fracarb870
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Comment: C: Adding UMAP coordinates to metadata
... Check the edited answer ...
written 4 months ago by fracarb870
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Answer: A: Adding UMAP coordinates to metadata
... In Seurat 3, you can export the coordinates to a dataframe using `Embeddings()`. `umapCoord <- as.data.frame(Embeddings(object = AD007[["umap"]]))` You can then add the PC columns to the `meta.data` as you please (`cbind`, `sapply`, `paste(..,collapse=)`,...) For example, if you only need to ...
written 4 months ago by fracarb870

Latest awards to fracarb8

Scholar 4 months ago, created an answer that has been accepted. For A: Adding UMAP coordinates to metadata
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Adding UMAP coordinates to metadata

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