User: g.k
g.k • 0
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Posts by g.k
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4
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... 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 ...
written 4 months ago by
g.k • 0
• updated
3 months ago by
Bioconductor Community ♦♦ 0
0
votes
2
answers
215
views
2
answers
... It is giving me incorrect number of dimensions
...
written 6 months ago by
g.k • 0
0
votes
2
answers
215
views
2
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... 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] ...
written 6 months ago by
g.k • 0
2
votes
1
answer
260
views
1
answer
... 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] + | ...
written 7 months ago by
g.k • 0
• updated
7 months ago by
James W. MacDonald ♦ 49k
0
votes
0
answers
243
views
0
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... 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 ...
written 12 months ago by
g.k • 0
0
votes
1
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290
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1
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... Yes I do consider them overlapping if they overlap by 1 position. Thank you I used findOverlaps() and it worked perfectly !
...
written 12 months ago by
g.k • 0
1
vote
1
answer
290
views
1
answer
... 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 ...
written 13 months ago by
g.k • 0
• updated
13 months ago by
Michael Lawrence ♦ 10k
0
votes
1
answer
334
views
1
answer
... 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?
...
written 22 months ago by
g.k • 0
• updated
22 months ago by
Axel Klenk • 920
1
vote
1
answer
2.4k
views
1
answer
... 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
...
written 22 months ago by
g.k • 0
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