User: mattkarikomi

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Posts by mattkarikomi

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Processor count for cores with Intel hyper-threading in differentialGeneTest()
... The documentation for Monocle 2 discusses the use of multiple cores for differential gene expression. Will I be able to use each virtual core on a hyper-threaded processor? For instance, if I had an 8-core Xeon W, would I be able to make the following call: differentialGeneTest(, cores=14) D ...
hpc monocle hyperthreading rna-seq written 5 days ago by mattkarikomi0 • updated 5 days ago by himanshuarya91620
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Given two sets of nucleotide n-mers, how can I learn sets of 'motifs' which are present in one and not the other?
... I have some unpublished data on DNA methylation, suggesting that there are differences in maintenance methylation efficiency at different sites from one cell cycle to another. I have a very coarse-grained approach for dividing the methylated sites into "likes to be methylated" and "really likes to ...
sequencing tf dna-methylation written 6 weeks ago by mattkarikomi0
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Comment: C: Linking patient survival to gene-set analysis
... Thanks Kevin, removing the transcript suffix allowed me to map them to Entrez IDs as Ensembl genes. ...
written 7 weeks ago by mattkarikomi0
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Comment: C: Linking patient survival to gene-set analysis
... Hi Kevin, You responses prompted me to think a bit more about what exactly I am trying to show. In particular your suggestion about clustering led me to several important works that have already been published. I've come up with a new workflow that incorporates this type of analysis, but hit one s ...
written 7 weeks ago by mattkarikomi0
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Comment: C: GDC API query to map HT-seq FPKM UUID to a Case UUID
... Hi Kevin, Those suggestions solved the problem. I ended up just renaming the columns in the RNA seq matrix generically, then building a lookup table for the file names. Now I have several questions about the analysis of this data and I created a second post to address these. Would you be willing ...
written 7 weeks ago by mattkarikomi0
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Linking patient survival to gene-set analysis
... I have a bunch of HT-seq data from the TCGA and the accompanying clinical metadata. All the patients have cancer. At the end of the surveillance period, some of the patients are dead, others are not. Lets call the deceased patients group A and the surviving patients group B. Also I know when the ...
tcga gsea survival rna-seq written 7 weeks ago by mattkarikomi0 • updated 7 weeks ago by Kevin Blighe11k
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Comment: C: GDC API query to map HT-seq FPKM UUID to a Case UUID
... Hi Daniela, I think I obtained the right manifest and it includes records with relevant parts of the data model, but somehow I am still failing to match my files to patient IDs. I have updated my post above. Can you take a look? Thanks for all your help! ...
written 8 weeks ago by mattkarikomi0
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Comment: C: GDC API query to map HT-seq FPKM UUID to a Case UUID
... Hi Kevin, I've used the downloaded manifest strategy above with limited success. Can you have a look? ...
written 8 weeks ago by mattkarikomi0
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GDC API query to map HT-seq FPKM UUID to a Case UUID
... I have a bunch of FPKM normalized mRNA sequencing from TCGA-PAAD, which covers pancreatic cancer patients. I wrote a script which goes through that data and makes a big data frame with all 60k+ Ensemble mappings for all 180+ patients, so that I can analyze various hypotheses regarding the clinical ...
R tcga gdc rna-seq written 8 weeks ago by mattkarikomi0

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