User: Martombo

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Martombo2.3k
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Seville, ES
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Posts by Martombo

<prev • 278 results • page 1 of 28 • next >
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Answer: C: DESEQ2 control vs multiple treatment
... you can specify the samples to test in the function results() results(dds, contrast = c("condition", "Drug1", "Control")) "condition" here is the name of the factor in your colData object. Once you have the individual results for each drug you can compare the log2FC you get and the number of s ...
written 2 days ago by Martombo2.3k
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Comment: C: Weird error in R
... is there no problem with your internet connection? ...
written 7 days ago by Martombo2.3k
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Comment: C: Find out the mutation type from TCGA data
... Isn't this copy number data? ...
written 9 days ago by Martombo2.3k
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Comment: C: For Generating PPI
... Why would you blast your gene sequences? STRING database has got human-specific entries. You can download the whole network from their website. ...
written 12 days ago by Martombo2.3k
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Comment: C: Low mapping percentage with TopHat
... What options did you use? Did you take care of applying the same rules for reporting an alignment? ...
written 12 days ago by Martombo2.3k
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Comment: C: unable to count reads that are aligned to coding region
... This is a sub-optimal way to count your transcripts, because you will have plenty of reads that are mapped to more than one transcript and you can either count them all or filter them out. Other tools like RSEM try to estimate the proportion of reads that are originating from each transcript. Better ...
written 13 days ago by Martombo2.3k
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Comment: C: GSEA on single-cell cluster data
... [GSVA][1] tries to estimate the pathway expression levels in every individual sample and then allows you to perform comparisons or unsupervised analysis like clustering on the transformed matrix. [1]: https://bioconductor.org/packages/release/bioc/html/GSVA.html ...
written 14 days ago by Martombo2.3k
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Comment: C: RSEM tool installation error
... You're missing GNU C++ compiler (g++). Install that with apt and everything should work. You could also use a docker image like [this one][1]. [1]: https://hub.docker.com/r/genomicpariscentre/rsem/~/dockerfile/ ...
written 14 days ago by Martombo2.3k
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Comment: C: Advice on running a differential expression analysis on patients with slightly d
... One important thing you can do in your analysis is to try to estimate the number and identity of co-variates in your samples. The aim would be to control for other variables that influence the gene expression, beside the specific mutation you're interested in (for example, as you mentioned, mutation ...
written 16 days ago by Martombo2.3k
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Comment: C: Tophat2 or STAR for IsoformSwitchAnalyzeR analysis
... Yes you are right. If you need to perform isoform discovery / transcriptome assembly the suggested pipeline nowadays is HISAT, StringTie, Ballgown. If you are studying a model organism (eg human, mouse), I would however suggest you to rely on the reference (Ensembl tends to be really extensive) and ...
written 21 days ago by Martombo2.3k

Latest awards to Martombo

Commentator 10 days ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 8 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Scholar 8 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 9 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Popular Question 9 months ago, created a question with more than 1,000 views. For different output format in Clustal-Omega
Scholar 10 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Appreciated 15 months ago, created a post with more than 5 votes. For A: Tophat --max-multihits option
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Great Question 17 months ago, created a question with more than 5,000 views. For Sjdboverhang Option In Star
Appreciated 19 months ago, created a post with more than 5 votes. For A: Tophat --max-multihits option
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Popular Question 2.2 years ago, created a question with more than 1,000 views. For different output format in Clustal-Omega
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Popular Question 2.4 years ago, created a question with more than 1,000 views. For misc_RNA in Ensembl
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 2.7 years ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Commentator 2.8 years ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?

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