User: sim.j.baum

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sim.j.baum50
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Posts by sim.j.baum

<prev • 21 results • page 1 of 3 • next >
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Answer: A: lift over gene ids rat to human
... I took another route: library(msigdbr) m_df = msigdbr(species = "Rattus norvegicus") m_df_sub = m_df[,c(5,8)] # select only the gene ids necessary m_df_sub_dis = distinct(m_df_sub) # remove non unqique rows df = merge(x = df, y = m_df_sub_dis, 'gene_symbol', al ...
written 4 months ago by sim.j.baum50
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lift over gene ids rat to human
... Hi, I am seeking to lift over gene IDs from rat to human, this is what I got: library("biomaRt") human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") rat = useMart("ensembl", dataset = "rnorvegicus_gene_ensembl") x = c("Tll1", "Tlx3") # gene list to lift over ge ...
R biomart rna-seq written 4 months ago by sim.j.baum50 • updated 4 months ago by Mike Smith1.6k
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Comment: C: topGO analysis "MF" term error
... Thank you Lluis, it was very silly, it is a miss assignment of a variable. I used the GOdata variable to calculate the GO terms values, but used another variable (sampleGOdata) later. From this I got the error. Should I delete this post? ...
written 5 months ago by sim.j.baum50
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topGO analysis "MF" term error
... Hi all, I am using topGO in R to get GO terms from a set of genes (in rat organism). I am mainly following the workflow described here: http://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf example of some entries in my gene list: int.genes_2: Sap25: 0 Sap30: 0 ...
R topgo rna-seq go written 5 months ago by sim.j.baum50
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Comment: C: unit scale in plotprofile plot - deeptools2
... Thank you. Its a related question, but could probably fill a seperate question: RPKM vs RPGC? Both normalization methods are fine to use in the work stream performed above? ...
written 11 months ago by sim.j.baum50
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unit scale in plotprofile plot - deeptools2
... Hi all, I generated a plot via deeptools2 with the folliwing steps: BamCoverage to generate a bigwig file from my bam file with default conditions plus --normalizeUsing RPKM Next, i created a matrix at the regions of interest with computeMatrix and then used plotProfile to visualize this. ...
chip-seq deeptools2 written 11 months ago by sim.j.baum50 • updated 11 months ago by Devon Ryan97k
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Comment: C: MACS2 "total fragments in treatment" gives less number of fragments than expecte
... What was surprising to me is: > maximum duplicate fragments in treatment = 1 > Redundant rate in treatment: 0.99 which are very high. My guess is that you have lots of PCR duplicates in your library. Therefore, the majority of your fragments are filtered out, I think. But lets wait ...
written 12 months ago by sim.j.baum50
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Answer: A: DiffBind to call differential binding of Super-enhancers from ROSE
... I think I know what you mean: I used deeptools2 for that - and it is similar to figures published by Loven J. et al. 2013 in Cell I think - they show the difference of the average binding in different conditions at SE and normal enhancer. If so you take A.) the BED SE file and get the median or ...
written 12 months ago by sim.j.baum50
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Comment: C: Which one to use for ChipSeq replicate comparison: Spearman or Pearson
... Very nice answer. What you can also do is to select `multiBamSummary BED-file --BED selection.bed --bamfiles file1.bam file2.bam -o results.npz` and use a BED-file if you have already genomic regions of interest. ...
written 12 months ago by sim.j.baum50
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Answer: C: deep learning predict gene expression
... A very interesting topic IMO. I think there is no easy answer to your question because you would need a lot of multi-dimensional data to say that element A is regulating gene B - and you would need functional validation with wet-lab experiments. However, what came to my mind is ChromHMM (http://comp ...
written 12 months ago by sim.j.baum50

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Popular Question 3.9 years ago, created a question with more than 1,000 views. For XLOC ID to GeneIDs

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