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Recent Replies
Comment: Genbank File Format
by
alenew.am
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Yes, it would be fine with an external solution, thanks for the reply
Answer: Polishing genome assembly
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Michael
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If you have Hifi reads your error rate should already be quite good, therefore polishing with potentially longer and slightly more error-pr…
Comment: Integrate transcriptomic data and proteomics data.
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Lluís R.
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You don't need to subset for common features, there are tools that work for that like RGCCA, mixOmics. See for instance a classification [h…
Answer: Integrate transcriptomic data and proteomics data.
by
KABILAN
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You can use R package named 'mixOmics' to integrate the datasets. Kindly go through the manual of this package.
Comment: Need help for downloading arabdopsis thaliana reference genome fasta file and gt
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Michael
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You will have to describe your problem in much more detail, we are unable to understand what the problem even is. > Please, anyone, sugge…
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Sudip
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Thank you.
Comment: MA plot of shrunken fold change
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ATpoint
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You will need to relevel to make all comparisons available as coefficients, see https://www.biostars.org/p/448959/, or just use ashr shrink…
Comment: Integrate transcriptomic data and proteomics data.
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ATpoint
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I have yet to see the fancy integration tool that can really do anything other than subsetting both datasets to the common genes/proteins/p…
Comment: Integrate transcriptomic data and proteomics data.
by
Ram
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Please define "combine" and "integrate" as best as you can. How do you picture the final product of this task?
Comment: NGS forensics: how to know if data is fabricated
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Philipp Bayer
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just k-mer counts (HashingVectorizer + Naive Bayes Classifier). I stayed away from looking at quality scores so far, simulators are usually…
Comment: Landmark gene selection in L1000.
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kim
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thank you for reply, but i want some information for what microarray data are selected for L1000. thank you!
Comment: Why cd-hit-est not work when sequence identity threshold<0.95?
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weidonglu
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The reason for your problem was most likely due to you relative complex data and too little system memory. For 20000-30000 transcriptome se…
Comment: Perfom a Gene Ontology Analysis from GO terms txt file
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sansan_96
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Your table should look like this (GO terms): ``` geneid GOid Zm00001eb000010 GO:0003690;GO:0003727;GO:0019843;GO:0005739 Zm00001eb000020 G…
Answer: Perfom a Gene Ontology Analysis from GO terms txt file
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sansan_96
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I understand, here is an example with topGO where you need a differential expression table (DESeq2 for example) and a table of GO terms: `…
Comment: Perfom a Gene Ontology Analysis from GO terms file
by
Hamtaro
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Thank u for your reply. The problem is that I used the genome and gene annotation from that webpage, not ensemble or ncbi, so I have to use…
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