User: mattkarikomi

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mattkarikomi20
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Posts by mattkarikomi

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11
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4
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Mapping Ensembl Gene IDs with dot suffix
... I have a bunch of bulk mRNA sequencing pulled off of the TCGA. Feature names appear to be Ensembl gene IDs with a suffix. Here is an example: > [995] "ENSG00000236246.1" "ENSG00000281088.1" [997] "ENSG00000254526.1" "ENSG00000223575.2" [999] "ENSG00000201444.1" "ENSG00000232573.1" I ...
gene ensembl biomart bioconductor written 3 months ago by mattkarikomi20 • updated 7 weeks ago by PavolG0
0
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1
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167
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1
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kmeans error when running reduceDimension(reduction_method = 'DDRTree')
... After setting my ordering filter, I run: > colonTumor <- reduceDimension(colonTumor, max_components = 3, > norm_method = c("none"), reduction_method = 'DDRTree', verbose=TRUE) Then I get the following error: > Error in kmeans(t(Z), K, centers = centers) : initial centers are not > ...
irlba monocle kmeans ddrtree written 4 months ago by mattkarikomi20 • updated 4 months ago by Kevin Blighe21k
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450
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Answer: A: Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assa
... turned out that fd was prepared based on a bad matrix. Issue resolved! ...
written 5 months ago by mattkarikomi20
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Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assayData
... As directed in the [Monocle 2 Documentation][1], the cellDataSet constructor is called on a sparse matrix and two AnnotatedDataFrames. Here is the suggested usage: pd <- new("AnnotatedDataFrame", data = sample_sheet) fd <- new("AnnotatedDataFrame", data = gene_annotation) cds < ...
celldataset monocle expressionset written 5 months ago by mattkarikomi20
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1
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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 months ago by mattkarikomi20 • updated 5 months 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 months ago by mattkarikomi20
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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 6 months ago by mattkarikomi20
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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 6 months ago by mattkarikomi20
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2
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549
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2
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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 months ago by mattkarikomi20
5
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544
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6 follow
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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 months ago by mattkarikomi20 • updated 6 months ago by Kevin Blighe21k

Latest awards to mattkarikomi

Scholar 5 months ago, created an answer that has been accepted. For A: Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assa

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