User: Sudeep

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Sudeep1.6k
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Posts by Sudeep

<prev • 186 results • page 1 of 19 • next >
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Answer: A: topGO apporach for a list a genes without expression
... I do not see any problems as such with your R code, but instead of using the function, you can also use a vector of gene ids as inputs. Have a look at this topGO vignette esp. sections 4.4 through 4.6 ...
written 4.2 years ago by Sudeep1.6k
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Answer: A: Gene set enrichment tool for RNA-Seq in Python?
... The top two results for googling "GSEA python" were these libraries: pygsa  and geseabase, and as Adrian already told you the analysis is independent of probeids. You will find the data format guides for GSEA and for pygsa library here: GSEA data format guide ...
written 4.5 years ago by Sudeep1.6k
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Answer: A: Using GO terms from Uniprot or Interpro?
... Since you didn't say the species you are interested in, I'm assuming that you are talking about human annotatoins. There was a post along the samelines in Biostar sometime before, see here: see it here ...
written 4.6 years ago by Sudeep1.6k
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Comment: C: Fitting Distribution Of The Gene Expression Levels Of Rna Seq Data
... This post in ResearchGate might be helpful ...
written 4.8 years ago by Sudeep1.6k
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Comment: C: Database Error When Running Blastn
... Did you try running blastn -query myquery -db mydatabase.fasta without .nhr suffix ? I suppose that your sequence database name is mydatabase.fasta ...
written 4.9 years ago by Sudeep1.6k
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Answer: A: How Did You Learn Good Practice In Bioinformatics/Computational Biology?
... This might also be a good read: How Not to Be a Bioinformatician ...
written 4.9 years ago by Sudeep1.6k
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Comment: C: Error In Installing Deseq
... /usr/bin/ld: cannot find -lgfortran collect2: error: ld returned 1 exit status Are you sure that fortran libraries are installed ? ...
written 4.9 years ago by Sudeep1.6k
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Methodologies, Pros And Cons Of Merging Multiple Expression Datasets
... Hi, I'm compiling a reading list for papers discussing methodologies, pros/cons of merging multiple gene expression data sets for meta analysis. So far, my list has these papers: Comprehensive analysis of correlation coefficients estimated from pooling heterogeneous microarray data Meta-analysis ...
microarray written 4.9 years ago by Sudeep1.6k
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Comment: C: Using Bash For Gatk Pipeline
... I know, it doesn't make much sense here, but got used to using g in almost all the cases,can't help it :) ...
written 4.9 years ago by Sudeep1.6k
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Comment: C: Using Bash For Gatk Pipeline
... I have edited my original post ...
written 4.9 years ago by Sudeep1.6k

Latest awards to Sudeep

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