Moderator: Kevin Blighe
Kevin Blighe ♦ 21k
- Reputation:
- 21,140
- Status:
- Trusted
- Location:
- University College London Cancer Institute
- Website:
- https://github.com/kev...
- Last seen:
- an hour ago
- Joined:
- 9 months, 3 weeks ago
- Email:
- k**********@outlook.com
Irish bioinformatician and Senior Research Associate in Bioinformatics at University College London Cancer Institute.
Previously worked in USA, Italy, Malta, Brazil, UK, and Ireland.
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There are mountains in our way... but we climb a step every day...
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Nella fantasia, io vedo un mondo giusto; Lì, tutti vivono in pace e in onestà...
Io sogno d'anime che sono sempre libere
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Give me one moment in time, when I'm more than I thought I could be...
Posts by Kevin Blighe
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Comment:
C: GDC server down???
... What exact commands have you both tried? It's possible that the data has just shifted to a new location. The TCGA data is constantly being refined.
Also, which R and package versions? ...
written 2 hours ago by
Kevin Blighe ♦ 21k
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... The user did indeed indicate that it worked: https://www.biostars.org/p/320699/#320940
Can you clarify, ttom? ...
written 4 hours ago by
Kevin Blighe ♦ 21k
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... Yes, is everything now okay, in that case? ...
written 5 hours ago by
Kevin Blighe ♦ 21k
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...
> 1. How to link Patient ID from "miRNA gene quantification" data where it is TCGA-G9-6356-01A-11R-1788-13 with "clinical" file which contains
> "TCGA-G9-6356" as Patient ID ?
In the general basic clinical metadata, there is only 1 entry per individual. Each individual is identified by the ...
written 22 hours ago by
Kevin Blighe ♦ 21k
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Comment:
C: SNP + INDEL Merging Guidelines
... Yes, I believe GATK's CombineVariants is the answer. ...
written 22 hours ago by
Kevin Blighe ♦ 21k
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... The error occurs when you attempt to perform operations on objects of unequal dimensions. For example:
c(1, 2, 3, 4) * c(10, 10, 10)
[1] 10 20 30 40
Warning message:
In c(1, 2, 3, 4) * c(10, 10, 10) :
longer object length is not a multiple of shorter object length
c(1 ...
written 1 day ago by
Kevin Blighe ♦ 21k
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... That's weird. Which parallel package version have you used? The authors do advertise that the function is parallel processing enabled?
I had to edit the clusGap function in order to make it parallelised. Took a day to figure it out: https://github.com/kevinblighe/clusGapKB
The authors never advert ...
written 1 day ago by
Kevin Blighe ♦ 21k
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... Calling Zhilong Jia ...
written 1 day ago by
Kevin Blighe ♦ 21k
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... Good point, zx8754 ...
written 1 day ago by
Kevin Blighe ♦ 21k
Latest awards to Kevin Blighe
Teacher
2 hours ago,
created an answer with at least 3 up-votes.
For A: Compare two columns of same file as paired rows
Scholar
6 hours ago,
created an answer that has been accepted.
For A: Cuffcompare output: thousands of novel transcripts
Scholar
1 day ago,
created an answer that has been accepted.
For A: Cuffcompare output: thousands of novel transcripts
Teacher
1 day ago,
created an answer with at least 3 up-votes.
For A: Cuffcompare output: thousands of novel transcripts
Scholar
1 day ago,
created an answer that has been accepted.
For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Good Answer
2 days ago,
created an answer that was upvoted at least 5 times.
For A: Complex Heatmap: Changing order of clusters
Commentator
3 days ago,
created a comment with at least 3 up-votes.
For C: DESEQ analysis contain rlog formation?
Scholar
4 days ago,
created an answer that has been accepted.
For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Appreciated
6 days ago,
created a post with more than 5 votes.
For Network plot from expression data in R using igraph
Appreciated
7 days ago,
created a post with more than 5 votes.
For Network plot from expression data in R using igraph
Scholar
7 days ago,
created an answer that has been accepted.
For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Teacher
7 days ago,
created an answer with at least 3 up-votes.
For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Teacher
8 days ago,
created an answer with at least 3 up-votes.
For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Scholar
8 days ago,
created an answer that has been accepted.
For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Teacher
8 days ago,
created an answer with at least 3 up-votes.
For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Teacher
10 days ago,
created an answer with at least 3 up-votes.
For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Scholar
11 days ago,
created an answer that has been accepted.
For A: Compare two columns of same file as paired rows
Appreciated
12 days ago,
created a post with more than 5 votes.
For Network plot from expression data in R using igraph
Teacher
12 days ago,
created an answer with at least 3 up-votes.
For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Scholar
12 days ago,
created an answer that has been accepted.
For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Teacher
13 days ago,
created an answer with at least 3 up-votes.
For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Appreciated
13 days ago,
created a post with more than 5 votes.
For Network plot from expression data in R using igraph
Teacher
13 days ago,
created an answer with at least 3 up-votes.
For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
Teacher
13 days ago,
created an answer with at least 3 up-votes.
For A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?
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