User: g.k

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g.k0
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Posts by g.k

<prev • 10 results • page 1 of 1 • next >
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Fisher test in Rna seq
... Hello, I would like to do rna seq data for several genes, tested in control and treatment. To do fisher.test I need a contingency table for each gene, is there a way to do this in R instead of computing a contingency table for each gene? I am new to this so any advice can be helpful. I have the ...
rnaseq R rna-seq written 12 months ago by g.k0 • updated 4 months ago by Gordon Smyth39k
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Comment: C: Selecting columns form a list of grange objects
... It is giving me incorrect number of dimensions  ...
written 14 months ago by g.k0
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Selecting columns form a list of grange objects
... I have a list having granges as follows:     $     File1.bed               GRanges object with 3 ranges and 2 metadata columns:                seqnames    ranges strand |        name                   <Rle> <IRanges>  <Rle> | <character>            [1]    chr1   [ 4,  6]    ...
granges R grange written 14 months ago by g.k0
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Concatenate a list of genomic ranges
... Hello, I have a list having granges as follows: $File1.bed GRanges object with 3 ranges and 2 metadata columns: seqnames ranges strand | name score <Rle> <IRanges> <Rle> | <character> <numeric> [1] chr1 [ 4, 6] + | ...
genomicranges granges R written 15 months ago by g.k0 • updated 15 months ago by James W. MacDonald52k
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Detect Sites with Minimum Gap in GRanges Object
... Hello, I have a GRange object and I am using the findOverlaps() function inorder to control the minOverlap and maxGap. However I was wondering if there is a way to get the opposite? Is there a way to get the sites that have a  maxOverlap and the minGap?  seqnames     ranges        strand   chr1   ...
genomicranges granges R grange written 20 months ago by g.k0
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Comment: C: Detecting Overlaps within Grange Object
... Yes I do consider them overlapping  if they overlap by 1  position. Thank you I used findOverlaps() and it worked perfectly ! ...
written 20 months ago by g.k0
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Detecting Overlaps within Grange Object
... Hello, I have a Grange object which contains coordinates. I want to be able to remove the overlapping coordinates within the object following this rule : End(B) > Start(A) & End(A) > Start(B) so  I  remove Coordinate B For example : Chrom Start End Name Score Strand ...
iranges granges R grange written 20 months ago by g.k0 • updated 20 months ago by Michael Lawrence11k
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Comment: C: How to know which Microarray Technique was used to processes the files
... Thank You ! ...
written 2.5 years ago by g.k0
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How to know which Microarray Technique was used to processes the files
... Hello, I have problem with analyzing microarray data sets. I have the GSM files and the GPL used which is GPL570, but how can I know if it is a 1 or 2 colored microarray technique used? ...
microarray R affymetrix microarrays written 2.5 years ago by g.k0 • updated 2.5 years ago by Axel Klenk940
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MA plot in R
... hello, I want to draw an MA plot  using plotWithHighlights() in R, however there are 2 simple arguments needed for this function which I'm not understanding how to use: status, and values. If someone can help me with them and probably give an example it would be great. Thank you very much ...
R rstudio plotma written 2.5 years ago by g.k0

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For MA plot in R

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