User: Sander Timmer

gravatar for Sander Timmer
Sander Timmer700
Reputation:
700
Status:
Trusted
Location:
United Kingdom
Website:
http://www.sandertimme...
Last seen:
4 years, 2 months ago
Joined:
7 years ago
Email:
s***********@gmail.com

A PhD candidate at the European Bioinformatics Institute (EBI), the European Molecular Biology Laboratory (EMBL) and Cambridge University.

In Ewan Birney‘s team I am working on understanding genetic variation on both molecular and whole body phenotypes.

You can share social stuff with me easily on my Google plus: Sander Timmer

Posts by Sander Timmer

<prev • 49 results • page 1 of 5 • next >
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Act Convert Wig/Bam/Common_Format Into Signal Track (Signal Track)
... I want to use the ACT tool of the Gerstein lab (http://info.gersteinlab.org/ACT_Tool) and noticed that they use the sgr as input for their aggregator tool. Before hacking/slashing together some scripts is there anyway I can use the common tools out there (bedtools, bamtools, bioperl etc etc) to conv ...
wiggle convert written 5.2 years ago by Sander Timmer700 • updated 4.1 years ago by Biostar ♦♦ 20
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Calculate Ld Between 2 Loci
... I know there are several ways of calculating LDs using tools like plink when using genotyping data. In my case I've several different loci on the genome that show some sort of interaction. Some of these might have SNPs thus I could use the SNPs LD as a measure though in many other cases I don't have ...
ld written 5.4 years ago by Sander Timmer700 • updated 5.4 years ago by Ryan D3.3k
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Comment: C: List Of Image Analysis Software
... Depends a bit also about what kind of images you have.... For MRI scans I'd suggest different software than for stained cell images! ...
written 5.8 years ago by Sander Timmer700
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Comment: C: Permutation Based Thresholds For Eqtl Analysis?
... What I always still wonder with this kind of FDR approach is that it sounds like you're very very tough on getting your Null distribution by always taking the most negative (as in worse for your FDR) from each permutation and using this in your ranking. But indeed this seems to be the standard way o ...
written 5.8 years ago by Sander Timmer700
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Comment: C: Circos Histogram Bam File
... Great, thanks a lot this is exactly what I was looking for! ...
written 5.9 years ago by Sander Timmer700
18
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7 follow
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Circos Histogram Bam File
... I've a BAM that I'd like to show its coverage off in a circos plot (http://circos.ca/documentation/tutorials/2d_tracks/histograms/images) Is there a standardised way of going from a BAM file towards such a histogram in circos? ...
bam written 5.9 years ago by Sander Timmer700 • updated 3.7 years ago by Biostar ♦♦ 20
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Answer: A: Questions For Raw Dataset Of Gwas Prostate Cancer
... For the WTCCC you just can ask for access to the data here: https://www.wtccc.org.uk/info/access_to_data_samples.shtml Should be not to hard for a researcher I presume as I expect that part of their funding is stating that they have to share this data. As you're interested in prostate cancer I d ...
written 6.0 years ago by Sander Timmer700
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Union Peaks For Peaks Called On Different Strains
... For a bunch of strains we have Chip-Seq on which we have been calling peaks using SWEMBL. We now want to generate an union peak set and I was wondering if people can shed some insight into this and things I should consider. Is there a "standardised" way of doing this? If not, when do you merge pe ...
chip-seq written 6.0 years ago by Sander Timmer700 • updated 6.0 years ago by Sukhdeep Singh9.3k
0
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Comment: C: Public Rnaseq/Dnaseq Data
... normally people would just call that sequencing or if you're just interesting in the variation (like SNPs) genotyping. ...
written 6.2 years ago by Sander Timmer700
4
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2.9k
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Answer: A: Public Rnaseq/Dnaseq Data
... This recent paper in Nature they have RNA-seq and DNase-seq for 70 YRI lines that are also part of the HapMap (and most 1000 genomes) LCLs. http://www.nature.com/nature/journal/v482/n7385/full/nature10808.html Data from this paper can be found here: http://eqtl.uchicago.edu/Home.html /edit, if I ...
written 6.2 years ago by Sander Timmer700

Latest awards to Sander Timmer

Appreciated 4.3 years ago, created a post with more than 5 votes. For A: Links To Good Next Gen Sequence Analysis Training Courses And Centres
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Circos Histogram Bam File
Supporter 4.3 years ago, voted at least 25 times.
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Public Rnaseq/Dnaseq Data
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: How To Analyse Snp Data
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Links To Good Next Gen Sequence Analysis Training Courses And Centres
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: How To Map Gene Id Or Gene Symbol To Locus
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: How To Show The Name Of Genes On Manhattan Plot
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: How To Find Nearest Gene To A Batch Of Snps
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: R Data.Frame To Latex Table With Formatting Of Decimal Points
Student 4.3 years ago, asked a question with at least 3 up-votes. For Using Biological Replicates To Filter Growth Dependant Probes In Microarray Experiments
Student 4.3 years ago, asked a question with at least 3 up-votes. For 1000 Genomes Low Coverage Data Inside A Gwas Study
Student 4.3 years ago, asked a question with at least 3 up-votes. For Calculate Ld Between 2 Loci
Student 4.3 years ago, asked a question with at least 3 up-votes. For Circos Histogram Bam File
Autobiographer 4.3 years ago, has more than 80 characters in the information field of the user's profile.

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