User: floriandeckert

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Posts by floriandeckert

<prev • 11 results • page 1 of 2 • next >
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DSS DMLTest Prior Estimate of theta dispersion
... Hello,  I want to calculate the prior estimation of the dispersion parameter theta but having some problems. Any help highly appreciated.  What the paper tells me In the DSS Bayesian hierarchical model, the biological variation among replicates of a group is captured by the beta distribution. The ...
bayesian dss methylation statistics dmltest written 6 months ago by floriandeckert30
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DSS DMLtest Object features
... Hello,  I am wondering what features are hold with the DSS DMLtest. class(DMLtest) reports a "data.frame" "DMLtest". Indeed, if I manipulate the DMLtest object, consequently being only a data.frame, it is not possible to perform callDMR no more.  I read the manuals but can't find any hint if there ...
dss dmltest written 7 months ago by floriandeckert30
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Answer: A: ensembldb from M.musculus NCBI37 v67 gtf
... Hi Johannes, thank you very much for taking the time helping me! Everything works super smoothly now. Awesome and thank you again!  ...
written 8 months ago by floriandeckert30
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Answer: A: ensembldb from M.musculus NCBI37 v67 gtf
... Thank you very much for your support Johannes! I followed your suggsetion and added exon_id to a GRange Object loaded from the gtf file. Then I used ensDBFromGRanges:  DB=ensDbFromGRanges(gtfGRmanip,                      outfile="Ensembl/manipulated/Mus_musculus.NCBIM37.67.splite",                  ...
written 8 months ago by floriandeckert30
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Comment: C: ensembldb from M.musculus NCBI37 v67 gtf
... Thank you very much!  ...
written 8 months ago by floriandeckert30
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Comment: C: ensembldb from M.musculus NCBI37 v67 gtf
... loaded via a namespace (and not attached):  [1] SummarizedExperiment_1.8.1    progress_1.1.2                lattice_0.20-35               htmltools_0.3.6                [5] yaml_2.1.16                   interactiveDisplayBase_1.16.0 blob_1.1.0                    XML_3.98-1.9                   [9] rl ...
written 8 months ago by floriandeckert30
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Comment: C: ensembldb from M.musculus NCBI37 v67 gtf
... > sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 [4] LC ...
written 8 months ago by floriandeckert30
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Answer: A: ensembldb from M.musculus NCBI37 v67 gtf
... Hi Johannes,  Thank you very much for your quick response!  Right now I am working with makeTxDbFromGFF. The problem is, that makeTxDB drops many of the metadata columns e.g. biotype. As far as I am concerned, it is not possible to add columns to makeTxDB since GenomicFeatures functions like trans ...
written 8 months ago by floriandeckert30
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ensembldb from M.musculus NCBI37 v67 gtf
... Hello  I am trying to perform a integrated analysis (RNAseq, ChIP, WGBS). To do so, I want to construct a custom annotation base which consists of GRange Objects with extra meta data columns for filtering (number of overlapping genes, methylation data, promoter status etc.). I am quite successful b ...
ensembl ensembldb ncbi37 v67 written 8 months ago by floriandeckert30
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DSS CpG coverage threshold
... Hello!  Since I do not have biological replicates I want to call DMRs with DSS. As far as I understand, first a basic smoothing is performed before using a beta-binominal GLM that takes biological and technical variance e.g. read-depth into account.  I have to admit, that I have not fully understa ...
coverage dss wgbs written 12 months ago by floriandeckert30

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