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Looping over several files in bash
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If we save the script pasted in the main post as a sh file and we have some .vcf files in a folder, by this line we can iterate over vcf files to extract what mentioned in the script returning .txt ...

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How I debug this code?
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2 votes

The problem was I should use ENTREZ rather than gene symbols

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How I can test my hypothesises computationally
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2 votes

The answer is behind these papers: The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution Single-cell mapping of gene expression landscapes and lineage in the zebrafish ...

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The visualisation of a list of genes on URD object
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1 votes

I just added URD clustering labels for each cel to seurat object and then I did DoHeatmap by using group.by="URD clustering labels"

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Why DoHeatmap Does not show all genes in genes.use?
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1 votes

https://github.com/satijalab/seurat/issues/287 In this post there is a answer for my question, however when I set scale to FALSE again the number of genes did not change but the shape of plot ...

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Calculating the number of probes for a given genomic range
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This command gave me the number of axons I hope this is correct Please correct me if I am wrong how_many_in_range <- function(coords){ coords = as.vector(coords) sum(...

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Getting this information for GISTIC2
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Depends on the software to generate the segmentation file; For example I have used scatngs for segmentation that for sample returns Segment number Chromosome Start position (origin-1) End position (...

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Variant calling without matched normal sample
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Here is a clue by scatngs https://github.com/cancerit/ascatNgs/wiki/Human-reference-files-from-1000-genomes-VCFs and already calculated file is here ftp://ftp.sanger.ac.uk/pub/cancer/support-files/...

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How to find correlation between two specific genes in same dataset?
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You can represent, and calculate, the correlations using psych: library(psych) pairs.panels(df,df, method = "pearson", # correlation method hist.col = "#00AFBB", ...

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A strange error while clustering of single cell RNA-seq using URD package
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-1 votes

This solved the error object <- URD::graphClustering(object) By this function I am telling R to use the graphClustering() function from the URD namespace. I probably had loaded another package ...

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Removing common variants in the 1000 genomes database from .vcf
-4 votes

Think removing everything < 0.05 from 1000g2015aug_all column of ANNOVAR annotation file helps with this

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