User: Samuel Brady

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Samuel Brady230
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Posts by Samuel Brady

<prev • 41 results • page 1 of 5 • next >
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Comment: C: How to search for consensus sequence in RNA-seq data?
... Great answer with lots of options and details. Thanks Alex. ...
written 8 weeks ago by Samuel Brady230
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Answer: A: cBioportal survival analysis help
... Unfortunately, there is no way to do this in cBioPortal. cBioPortal will call patients with either up-regulation OR down-regulation "altered," while those with a z-score between -2 and 2 "non-altered." This of course makes no sense. If you'd like something simple, I'd use [KM plotter][1]. If you wa ...
written 8 weeks ago by Samuel Brady230
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Comment: C: mutation signatures from MAF's, and decompose them into Stratton signatures
... I've had a lot of success with the deconstructSigs package in R for determining Stratton mutation signatures. You may want to try that one instead as it may be more user-friendly. ...
written 8 weeks ago by Samuel Brady230
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Answer: A: ROC for biomarker discovery
... Yes, you can use the mean expression of 10 different miRNAs for ROC analysis. However: If you have tested (or will test) many different combinations of 10 miRNA sets to find one that classifies your samples well, you will want to have an external validation dataset to see whether (1) your biomarker ...
written 8 weeks ago by Samuel Brady230
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Answer: A: How to find RNASeq V2 RSEM normalized expression values for various cancer studi
... Often normal samples are mixed into TCGA data. Look at each of your sample barcodes, which will have the format TCGA-02-0001-***01***. If the bold italicized digits are between 10 and 19 it's a normal sample. If it's 01 it's a solid tumor. (See the TCGA barcodes [website][1].) I'm not sure if cBioP ...
written 8 weeks ago by Samuel Brady230
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Comment: C: From sam data, how do I tell from which fastq file each read came from?
... The read group ID sometimes encodes which fastq file the read came from. Check how many read group IDs you have and see if it matches the number of fastq files you expect. ...
written 8 weeks ago by Samuel Brady230
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Answer: A: Are there downloadable DBs for hotspot mutations?
... I don't know of a database. But you can ask whether your specific mutations are recurrent by querying cBio over the web, using Python. import urllib2 # get information on breast cancer "brca" mutations in gene PIK3CA cBioUrl = "http://www.cbioportal.org/webservice.do?cmd=getMutat ...
written 8 weeks ago by Samuel Brady230
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Answer: A: Is SNPeff still the standard for variant effect prediction?
... The tools I hear used most frequently are SnpEff, VEP, and Annovar. This [paper][1] (Table 1) shows a comparison of the three tools. SnpEff tends to be robust and I personally use it the most. Remarkably, SnpEff can effectively annotate even structural variants and long indels, in addition to trad ...
written 8 weeks ago by Samuel Brady230
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Answer: A: multi-omics data gene set enrichment analysis
... GSOA incorporates multiple types of omic data at a time. See the [paper][1] and [documentation][2] to use it in R. [1]: https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-015-0189-4 [2]: https://bitbucket.org/srp33/gsoa ...
written 9 weeks ago by Samuel Brady230
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Answer: A: Intronic Variant Filtering
... You can find the locations of exons (for hg19) from UCSC here: hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz Columns 10 and 11 show you the start and end sites, respectively, of exons. Make sure the genome build you are using matches the build you download from UCSC. ...
written 9 weeks ago by Samuel Brady230

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Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: how to do gene annotation
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Scholar 8 weeks ago, created an answer that has been accepted. For A: how to do gene annotation
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Scholar 9 weeks ago, created an answer that has been accepted. For A: how to do gene annotation
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