User: Mdeng

gravatar for Mdeng
Mdeng520
Reputation:
520
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Location:
Germany
Last seen:
2 years, 5 months ago
Joined:
7 years, 8 months ago
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m********@googlemail.com

Foo is not one bar.

Posts by Mdeng

<prev • 55 results • page 1 of 6 • next >
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Comment: C: Reference and dbSNP incompatibility issue (MuTect2)
... This is pretty useful. THX ...
written 2.4 years ago by Mdeng520
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Answer: A: FirebrowseR retrive all the genes expression
... Sadly the API is not designed for these purposes. It's likely more intended to provide a light interface for pre-build queries, which e.g. could be included in an application etc.. To bulk download data sets for an entire cohort I would recommend using [GDAC][1] or you could still user FirebrowseR ...
written 2.7 years ago by Mdeng520
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Answer: A: Point mutation as parameter in firebrowseR
... This is something that is not covered within the Firebrowse API and since FirebrowseR is just an API client, it's not within there as well. When you have your data.frame of your desired mRNA / APC samples at hand, just use the their "tcga_participant_barcode" column and run the "Analyses.Mutation.MA ...
written 3.1 years ago by Mdeng520
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Comment: C: data matrix from firebrowser figure
... The viewGene expression visualizer just uses the mRNA data available thru the Firehose API (see here). The RSEM Score they use for plotting is already included when retrieving data from the API. This is also said when you klick the "help" on your link. ...
written 3.1 years ago by Mdeng520
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Comment: C: TCGAs CNV (SNP Array) level 3 data, confusing descriptions
... Exactly. And for those which are controlled with a normal sample, the analysis pipeline is not clear to me. Let's say for one patient the region chr1:1000-1200 has a seqMean of 0.2 in the normal and 0.7 in the tumor sample. What do I get when download the T and N sample? Reading SNP array-based dat ...
written 4.6 years ago by Mdeng520
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TCGAs CNV (SNP Array) level 3 data, confusing descriptions
... Hello everyone, again I am struggling with getting TCGAs data and description together. As the title says, it's about CNV data by SNP Arrays. Reading the wiki page SNP array-based data it says, Level 3 data describes regions of the genome that seem to have segmental duplications or deletions in t ...
unpaired paired tcga cnv level3 written 4.6 years ago by Mdeng520 • updated 4.4 years ago by roelverhaak0
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Comment: C: Tcga: "Tumor, Matched Normal" Vs. "Normal, Matched Tumor"
... Yes, thank you. This should be written down somewhere within TCGAs wiki. ...
written 4.6 years ago by Mdeng520
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Comment: C: TCGAs Methylation Data Annotation
... Perfect, this is what I was looking for. Thanks you very much! ...
written 4.9 years ago by Mdeng520
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TCGAs Methylation Data Annotation
... Hello everyone, I got a question regarding TCGAs Methylation data. I downloaded it via the "Data Matrix", 98 Samples, 49 pairs of Tumor/Normal tissue, all Level 3 and all from Illuminas HumanMethylation450 Chip. Everything is prostate cancer. So, looking at the data, there ~25% of the symbols missi ...
annotation tcga methylation written 4.9 years ago by Mdeng520 • updated 4.9 years ago by Charles Warden6.5k
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Comment: C: Tcga: "Tumor, Matched Normal" Vs. "Normal, Matched Tumor"
... I know. by pure somatic SNPs I meant the preprocessed calculations on the SNPs to get the somatic SNPs. But it's just as you said, To work with somatic SNPs a pair of files needs to be downloaded. Thank you. ...
written 5.3 years ago by Mdeng520

Latest awards to Mdeng

Epic Question 2.7 years ago, created a question with more than 10,000 views. For Tcga: "Tumor, Matched Normal" Vs. "Normal, Matched Tumor"
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Grouping Cnv After Segmentation Using Bioconductor Dnacopy
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Go Terms From Ensembl
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: Tcga: "Tumor, Matched Normal" Vs. "Normal, Matched Tumor"
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Link Between Ensembl And Omim
Appreciated 3.6 years ago, created a post with more than 5 votes. For A: How To Make A Circular Plot Of Snps And Indels ??
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Work With Dnacopy (Bioconductor) And Varscan Copynumber Results
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Link Between Ensembl And Omim
Great Question 3.9 years ago, created a question with more than 5,000 views. For Tcga: "Tumor, Matched Normal" Vs. "Normal, Matched Tumor"
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Your Favorite Mapper For What Kind Of Data?
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Link Between Ensembl And Omim
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Your Favorite Mapper For What Kind Of Data?
Student 4.3 years ago, asked a question with at least 3 up-votes. For Your Favorite Mapper For What Kind Of Data?
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Tcga: "Tumor, Matched Normal" Vs. "Normal, Matched Tumor"
Appreciated 5.0 years ago, created a post with more than 5 votes. For A: How To Make A Circular Plot Of Snps And Indels ??
Good Answer 5.0 years ago, created an answer that was upvoted at least 5 times. For A: How To Make A Circular Plot Of Snps And Indels ??
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Using Gatk, Removing Read Contigs On Bam Level
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Varscan, Using The Copycaller
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Work With Dnacopy (Bioconductor) And Varscan Copynumber Results
Supporter 5.0 years ago, voted at least 25 times.
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Performance Bottlenecks In Next Generation Sequence Analysis Pipeline
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: How To Make A Circular Plot Of Snps And Indels ??
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: How To Get Ref.Fasta
Student 5.0 years ago, asked a question with at least 3 up-votes. For Your Favorite Mapper For What Kind Of Data?

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