User: moushengxu

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moushengxu270
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Posts by moushengxu

<prev • 165 results • page 1 of 17 • next >
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Answer: A: How to install a bioconductor package RMySQL and specify R parameters
... I was able to install CopywriteR after the following steps: 1. Download CopyhelpeR_1.0.2.tar.gz 2. sudo R CMD INSTALL CopyhelpeR*.tar.gz 3. sudo R CMD INSTALL CopywriteR*.tar.gz This somehow bypassed the RMySQL installation. Part of the problem might come from the R version: I was using R 3.2 ...
written 14 days ago by moushengxu270
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Comment: C: How to install a bioconductor package RMySQL and specify R parameters
... Thanks a lot for the input. I got almost identical errors after downloading the package. Weird because "mariadb-connector-c" is already installed by brew in the specified dir and the location is given at the command line. How come it still cannot find it? The command line: R CMD INSTALL --conf ...
written 15 days ago by moushengxu270
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How to install a bioconductor package RMySQL and specify R parameters
... I am trying to install CopywriteR, which failed at updating a dependent package RMySQL. The error I got was as follows: ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libmysqlclient was not found. Try installing: * deb: libma ...
software error R next-gen chip-seq written 15 days ago by moushengxu270
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Answer: A: How to generate a ROC curve for a dataset?
... You can generate 10 ROC curves with 10 AUC scores. AUC scores can be compared easily. ...
written 24 days ago by moushengxu270
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Comment: C: How can I make RSEM to align ChIPseq signal to the nearest gene?
... Could be Pol2, Histone modifications, ATAC, etc. For Pol2, usually we would be interested in +-5k from TSS; for histone modifications, ATAC, double strand breaks, ... , often you want to check the whole genome regardless how far/close the signal is to a gene. ...
written 28 days ago by moushengxu270
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Comment: C: How can I make RSEM to align ChIPseq signal to the nearest gene?
... Good question. Assign ChIP signals to genes. ...
written 28 days ago by moushengxu270
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How can I make RSEM to align ChIPseq signal to the nearest gene?
... I guess I can make a GTF by myself, and let the GTF associate genomic coordinates with genes. But assigning coordinates to closest genes is not a simple task. Overlapping gene regions can be problematic. Is there such a GTF available or is there an option to turn on/off with rsem-prepare-reference/r ...
gene next-gen alignment chip-seq sequencing written 29 days ago by moushengxu270
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How does RSEM allocate ChIPseq signals to genes?
... For RNAseqs, allocating the read seqs to genes is straightforward and easy: within the gene region or not. How about ChIPseqs? For instance, if you are mapping Pol2 signals to genes, and you care about +-5k TSS regions, can you tell RSEM to do such an association? Even more complicated, if you want ...
gene assembly next-gen chip-seq written 5 weeks ago by moushengxu270
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Comment: C: edgeR RNA-seq Results Across Conditions
... Can you post your code here? ...
written 3 months ago by moushengxu270
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Answer: A: Enrichment Analysis from DESeq2 data
... I use GSEA (Broad Institute). Just rank your genes by -log(P-value) * sign(logFC). ...
written 3 months ago by moushengxu270

Latest awards to moushengxu

Scholar 14 days ago, created an answer that has been accepted. For A: edgeR artifacts on p-value and/or fold change?
Popular Question 7 weeks ago, created a question with more than 1,000 views. For t-test or linear regression?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For edgeR and GO analysis using goana
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: SNPEFF for de novo transcriptome annotation
Popular Question 6 months ago, created a question with more than 1,000 views. For edgeR and GO analysis using goana
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Scholar 8 months ago, created an answer that has been accepted. For A: edgeR artifacts on p-value and/or fold change?
Scholar 12 months ago, created an answer that has been accepted. For A: edgeR artifacts on p-value and/or fold change?
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