User: orzech_mag

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orzech_mag220
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OrzechMag
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Posts by orzech_mag

<prev • 71 results • page 1 of 8 • next >
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Comment: C: Code for multiclass differential gene expression analysis
... Indeed, this is RNA-seq. Thank you for your suggestion, I think I'll do that as the method you mentioned are broadly recognized. Nevertheless, as my abilities to write functions are very poor and I am trying to learn something, I wish I could solve the presented issue anyway. Just for my knowledge. ...
written 8 months ago by orzech_mag220
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Code for multiclass differential gene expression analysis
... Dear Collegues, I am trying to perform analysis of differentially expressed genes between multiple groups. For that I found some tutorial (https://jef.works/blog/2017/05/31/multiclass-diffential-expression-analysis/). I am interested in t-test only between one group vs rest. This is corresponding c ...
function ttest deg written 8 months ago by orzech_mag220
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Comment: C: How to color nodes in Cytoscape according to expression of genes? How should the
... Hi, Aside of each color in the panel there are RGB values. You can write them down. Best regards! -------- Wiadomość oryginalna --------Temat: [biostar] How to color nodes in Cytoscape according to expression of genes? How should the input file look like?Od: Buffo on Biostar mailer@biostars.orgDo: ...
written 14 months ago by orzech_mag220
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Comment: C: Methods for contrasting gene expression profiles between multiple groups
... Thank you Kevin. It seems like there is wide range of options, now I need to define, which one will be appropriate for me. ...
written 16 months ago by orzech_mag220
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Comment: C: Methods for contrasting gene expression profiles between multiple groups
... Please correct me if I am wrong, but I don't feel like ANOVA will solve my issue. Now I realized that I didn't specified all significant details of the data. So, I have big cohort study: 800 patients divided into 4 groups (2 cancer subtypes divided into 2 smaller groups), each patient had sequenced ...
written 17 months ago by orzech_mag220
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Methods for contrasting gene expression profiles between multiple groups
... Dear Colleges, I've got rna-seq expression data in two subtypes of cancer divided into two smaller groups each (finally I am having 4 groups to compare). I would like to compare all 4 groups at once to see gene profiles that are common and different between all these groups. I'd like to ask you wha ...
expression profiling rna-seq written 17 months ago by orzech_mag220 • updated 17 months ago by Kevin Blighe66k
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Comment: C: How to color nodes in Cytoscape according to expression of genes? How should the
... The best are the easiest solutions, but the hardest to find. Dziękuję ;) ...
written 2.7 years ago by orzech_mag220
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Comment: C: How to color nodes in Cytoscape according to expression of genes? How should the
... Thanks scooter for suggestions. It does make sense for me. However I think that real issue lays in my experiment or workflow. I am afraid that I am not able to import the networks from STRING, because I have my own network that was created with another approach based on co-expression patterns. That' ...
written 2.7 years ago by orzech_mag220
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How to color nodes in Cytoscape according to expression of genes? How should the input file look like?
... Dear Colleagues, I would like to do some visualization of my network in Cytoscape. My file contains genes and their expression values in normal and tumor samples. The visualization of interest would be the same network colored according to A) expression in normal samples and B) expression in tumor ...
software degs cytoscape rna-seq expression written 2.7 years ago by orzech_mag220 • updated 2.7 years ago by a.zielezinski9.2k
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Comment: C: CAGEr BAM files size issue
... Dear Colleagues, via Bioconductor support I got the following reply: > The error message is coming from Biostrings and is admittedly not > helpful. I just changed this in Biostrings 2.44.2 and now it says: > > > unlist(big_dna_string_set) Error in .Call2("XStringSet_unlist", x, PAC ...
written 3.3 years ago by orzech_mag220

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