User: Martombo

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Martombo2.6k
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Posts by Martombo

<prev • 312 results • page 1 of 32 • next >
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Comment: C: GSEA pvalue output of 0.0. Can I make it more specific?
... The number of permutation gives you a upper bound on the "real" p-value. If you make 1000 you can say your real p-value < 0.001, if you make 10000 (and the output is 0 again) you can say it is < 0.0001. ...
written 2 days ago by Martombo2.6k
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Comment: C: What to use for estimation of transcription factors' activity based on RNAseq da
... You can use ARACNe and VIPER to estimate TF activity from expression data. The former builds a network of regulated genes and it was already run on most TCGA [data][1]. VIPER itself is accessible in a R [package][2]. [1]: https://bioconductor.org/packages/release/data/experiment/html/aracne.netw ...
written 3 months ago by Martombo2.6k
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Comment: C: RNAfold discriminant error
... you can check if one specific line is causing the problem, by using subsets of the input file ...
written 5 months ago by Martombo2.6k
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Comment: C: RNAfold discriminant error
... it may help if you can provide a reproducible example ...
written 5 months ago by Martombo2.6k
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Answer: C: Interpretation problem at PCA plot for detecting batch effect
... There are better ways to assess the presence of batch effects. First thing, FPKM is not a robust normalization method to compare different samples. Use the normalization methods of R packages like DESeq2 or limma-voom, it would then be more appropriate to look for a batch effect. You could also remo ...
written 8 months ago by Martombo2.6k
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Comment: C: predicting 3D structure of protein from DNA sequence
... I assume you have cDNA that can be easily translated to protein sequence? If so, you can perform an analysis called homology modelling. [Swiss-model][1] is an example of a simple tool that can do that. [1]: https://swissmodel.expasy.org ...
written 8 months ago by Martombo2.6k
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Comment: C: Maths implications: log2 transformation before or after normalisation
... Well it depends on the normalization, if it's quantile normalization it should not make a difference if you log transform before or after, provided you don't have negative numbers. ...
written 9 months ago by Martombo2.6k
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Answer: C: Bioinformatician, a jack of all trades, but in the eye of the CV-beholder a mast
... I believe there is generally some misconception about the amount of previous knowledge and technical skills that is expected from new employees. In every job, even the most competent person still needs to learn a lot. So the ability to learn and adapt to a new position is much more valuable. This is ...
written 9 months ago by Martombo2.6k
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Comment: C: gene_bodyCoverage.py No usable output...why?
... Alright, are you using bash? If so you can run an awk one liner to get the 12 column you need. Something along these lines should work: awk 'BEGIN{OFS="\t"}{$7=$2; $8=$3; $9="0,0,0"; $10=1; $11=$3-$2","; $12="0,"; print}' ...
written 10 months ago by Martombo2.6k
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Comment: C: gene_bodyCoverage.py No usable output...why?
... And yet, here we are ;) Just a general tip for bioinformatics: always check the results you get, you cannot simply trust any program blindly. Even popular formats like BED, GTF can have slightly different properties / requirements depending on the tool you are using. The error is telling you that t ...
written 10 months ago by Martombo2.6k

Latest awards to Martombo

Popular Question 10 weeks ago, created a question with more than 1,000 views. For human Natural Antisense Transcript database
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Comparative boxplots with R
Popular Question 4 months ago, created a question with more than 1,000 views. For human Natural Antisense Transcript database
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 11 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Scholar 13 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Epic Question 18 months ago, created a question with more than 10,000 views. For Sjdboverhang Option In Star
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Student 21 months ago, asked a question with at least 3 up-votes. For Sjdboverhang Option In Star
Popular Question 21 months ago, created a question with more than 1,000 views. For human Natural Antisense Transcript database
Commentator 22 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 2.5 years ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Scholar 2.5 years ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 2.6 years ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Popular Question 2.6 years ago, created a question with more than 1,000 views. For different output format in Clustal-Omega
Scholar 2.7 years ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Tophat --max-multihits option

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