User: Haci

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Haci120
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Posts by Haci

<prev • 18 results • page 1 of 2 • next >
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Answer: A: Pull number of cells in cluster from seurat object
... The cluster information is stored in the `@meta.data` slot and in a column something like `res.0.5` as you used a resolution of 0.5 in your `FindClusters()` call. If you re-run `FindClusters()` with another resolution parameter, an additional column will be added. To get the numbers in each cluster ...
written 4 days ago by Haci120
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Answer: A: file of CDSs
... The file `your_CDS.fasta` is being manipulated by `sed`, which makes use of regular expressions to do so in this case. Just go to a regex tester, for example https://regex101.com and paste `(^[^_]+)_.+` in the "REGULAR EXPRESSION" box for a detailed expression of what each part of the regex does. ...
written 7 days ago by Haci120
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Comment: C: Mapping Entrez gene ids to Ensembl ids
... Can you post the actual function that gives the error? Where is your `getBM()` call? ...
written 7 days ago by Haci120
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Answer: A: Gene Annotation in Bed file
... For disease related genes you might want to check [OMIM][1]. You would need to register to download data. For the gene coordinates, there are a few repos, Ensembl, UCSC. As far as I remember, you would need to retrieve gff (or) gtf from Ensembl and than convert to bed format. UCSC Table Browser enab ...
written 9 days ago by Haci120
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Answer: A: single cell data analysis
... If by "integration" you mean generating a single count table from two different datasets, you would need to add prefixes to your cell barcodes. I know that Seurat's `Merge()` (or sth like that) does it for you. If you mean "aligning" datasets so as to remove batch effects, etc, you might need to ch ...
written 9 days ago by Haci120
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Answer: A: Filter transcripts based on CDS length
... Whereas the solution offered by @EVR would be much faster, here is the `dplyr` equivalent: library(data.table) # for fread() library(dplyr) input %>% group_by(GenestableID)%>% filter(CDSLength == max(CDSLength)) %>% ungroup() # A tibble: 7 x 7 ...
written 11 days ago by Haci120
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Answer: A: Open Reading Frame in Biopython
... As far as I can see your code does not have a check for the starting methionine, you are retrieving ORFs that generate at least 100 amino acid long peptides. And I am pretty sure the 530 a.a. long "Genbank peptide" is within your 554 a.a. long peptide prediction. Check from 25th amino acid on in yo ...
written 11 days ago by Haci120
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Answer: A: Single cell clutering after regressing out cell cycle effect using seurat
... If you check [Seurat vignette on cycle cycle scoring][1] (the one compiled on 2019-06-24), you will see that there are basically two steps. First cell cycle scores (corresponding to S and G2M states) are calculated. These scores are then used to regress-out associated signal from the whole of the d ...
written 13 days ago by Haci120
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Comment: C: how to set Deseq factor
... If you don't have any replicates and 6 levels, you should use this as can be seen in my initial answer: > factor(1:6) [1] 1 2 3 4 5 6 Levels: 1 2 3 4 5 6 ...
written 14 days ago by Haci120
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Comment: C: how to set Deseq factor
... I suggest you double check your experimental design, which hopefully includes biological replicates. Just declare the levels according to the order of the levels in the count matrix. For example if first three are control do the following: > factor(c(rep("ctl", 3), rep("exp", 3))) [1] ct ...
written 14 days ago by Haci120

Latest awards to Haci

Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Subsetting a set of genes of interest from DESeq2 res
Scholar 14 days ago, created an answer that has been accepted. For A: Subsetting a set of genes of interest from DESeq2 res
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Subsetting a set of genes of interest from DESeq2 res

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