User: Haci

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Haci210
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Posts by Haci

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Seurat integration of two datasets - GSE126783
... `group.by` can be used the color data points according to the a column in the `meta.data` slot of a given Seurat object. `label` is tricky though, as far as I remember, the "labels" come from the "active identities" and this works fine if different identities are clustered separately, otherwise labe ...
written 4 days ago by Haci210
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Answer: C: Seurat integration of two datasets - GSE126783
... With your own code, you are already preparing two objects that are normalized and for those variable genes are calculated. In that sense you just need to put your `ctrl` and `LD` objects in a list with `your_list <- list(ctrl, LD)`. This new list can now be used for the integration as stated in t ...
written 8 days ago by Haci210
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Comment: C: best way to combine RNAseq data from different sequencing batches
... If you take a look at the source code of `collapseReplicates()`, you will see that there is a `rowSums()` call summing up gene counts per "group", so yes you can do so manually too. And you can also feed all of your FASTQ files (resulting from different runs) of a given sample to your aligner of c ...
written 11 days ago by Haci210
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Answer: A: Interpretation of hazard ratio
... Your intuition is correct, you need to look at `exp(coef)`, which is the `hazard ratio` and in your case the numerator is "upregulation" and the denominator is "downregulation". This hazard ratio of <1 shows that there is less chance of the event happening (in this case death) when your gene of i ...
written 18 days ago by Haci210
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Comment: A: featurecounts output changes the underscores in the sample name into dots
... `featureCounts()` of `Rsubread` does not generate `bam` files but uses them as input. You are probably using the `align()` function from the said package. If that is the case, you might want to check the `output_file` argument. Just change the default `output_file = paste(readfile1,"subread",outpu ...
written 22 days ago by Haci210
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Answer: A: How to get lists of genes for kegg pathways
... I can't offer a `Python` solution but here is some `R` code I have used in the past: library(org.Hs.eg.db) # Genome wide annotation for Human # org.Hs.egPATH contains Mappings between Entrez Gene identifiers and KEGG pathway identifiers kegg_paths <- as.list(org.Hs.egPATH2EG) ` ...
written 3 months ago by Haci210
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Comment: C: Cox proportional hazards regression use log2 fpkm
... I think your definition of heteroscedasticity is off, based on a typical "mean variance plot" from an RNA-seq experiment, you would see that the higher the mean counts the lower the variance. ...
written 3 months ago by Haci210
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Answer: A: R: Plotting MSMC/PSMC results using ggplot2
... I think you are looking for `geom_step()`, which would generate a "staircase plot". Just replace `geom_line()` with `geom_step()`. ...
written 3 months ago by Haci210
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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 5 months ago by Haci210
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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 5 months ago by Haci210

Latest awards to Haci

Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Subsetting a set of genes of interest from DESeq2 res
Supporter 22 days ago, voted at least 25 times.
Scholar 3 months ago, created an answer that has been accepted. For A: Subsetting a set of genes of interest from DESeq2 res
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Subsetting a set of genes of interest from DESeq2 res
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Subsetting a set of genes of interest from DESeq2 res
Scholar 5 months ago, created an answer that has been accepted. For A: Subsetting a set of genes of interest from DESeq2 res
Teacher 5 months 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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