User: Duckula

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Duckula20
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Posts by Duckula

<prev • 19 results • page 1 of 2 • next >
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Answer: A: Anndata: finding cells that express a specific gene
... Ok I found my answer :D It was not that complicated adata[:, adata.var_names.str.match('genenames')] ...
written 9 months ago by Duckula20 • updated 9 months ago by genomax72k
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Anndata: finding cells that express a specific gene
... Dear all, I am analyzing my single cell data using Scanpy package and as you may knwo it stores my data in anndata object which is a panda like data frame. I am interested to know which of my cells express the gene x. Does anyone has an idea how would I be able to access that information? I am not ...
python rna-seq written 9 months ago by Duckula20
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Comment: C: Transposing a .tsv count matrix
... My concern is that the data is too big in sense of size itself and doesn't have to do anything with memory because in R the Error message "allocate vector of size" indicate a limit on the object it self to be created. "The number of bytes in a character string is limited to 2^31 - 1 ~ 2*10^9, which ...
written 10 months ago by Duckula20
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Comment: C: Transposing a .tsv count matrix
... @WouterDeCoster Thanks for your comment! I actually tried to import my data in R and then transpose it from there but I faced the error "Error: cannot allocate vector of size 125 Kb" which also indicated that my data is transposed on a wrong side but now I couldn't even import it not even transpose ...
written 10 months ago by Duckula20
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Comment: C: Transposing a .tsv count matrix
... Well the problem is I can't open my file in usual apps like notepad++ or so. I have been trying to import my data into R but its still running ! that's why I actually switched to python and scanpy as it was saying its optimized for huge data which I found somehow correct because I was able to load m ...
written 10 months ago by Duckula20
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Comment: C: Transposing a .tsv count matrix
... Hi, Thanks for your reply, but if you see its indicating that n_var stands for 'n_cells' and according to that I am having 66882 cells with 4057 genes! That doesn't make sense also when I plot for my highly variable genes using provided function I see cell names instead of genes in my plot! ...
written 10 months ago by Duckula20
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Transposing a .tsv count matrix
... Dear all, I have a .tsv count matrix from a single cell experiment and I want to analyze it using SCANPy package in Python. When I import my data using following command mydata=sc.read("counts_expression_matrix.tsv",delimiter='\t',cache=True) I can see my data is stored as follow: > AnnData ...
python rna-seq scanpy written 10 months ago by Duckula20
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Error in converting seurat object to anndata class
... Hi everyone, I would like to convert my seurat object to an anndata format and for that I am using the following code Convert(from = Geissmann_Seurat, to = "anndata", filename = "Seurat_object_for_python.h5ad", chunk.dims = "auto", overwrite = F ...
python seurat rna-seq R written 11 months ago by Duckula20 • updated 10 months ago by Biostar ♦♦ 20
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(Closed) Sorting a matrix rowname based on column of another matrix
... Dear all, I have two matrices similar to below: a b c d id1 id2 id3 id4 1 2 3 4 b 1 2 3 6 7 8 9 c 0 2 4 d 1 2 2 a 5 6 8 And I want to sort the row name of th ...
R matrix written 11 months ago by Duckula20
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Averaging with technical and biological replicates
... Dear all, I have a data-set consisting of biological and technical replicates and I am interested to use the mean expression of them by initially having the mean of the technical replicates and then the biological replicates before analyzing my data-set using DESEQ2. I wonder if any of you have an ...
R next-gen deseq2 rna-seq written 12 months ago by Duckula20 • updated 12 months ago by zx87548.2k

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Scholar 9 months ago, created an answer that has been accepted. For A: Anndata: finding cells that express a specific gene

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