User: Learner

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Learner 80
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Posts by Learner

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how to make a graph from CoIP
... I am wondering if anyone can guide me toward this. we try to pull down a protein fo interest and we get what proteins come with it assuming that they belong to a complex. We have an abundance for each protein. lets say 100 proteins and 100 abundance. is there any way that I can make a network betwee ...
proteomics protein written 8 hours ago by Learner 80
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what data normaly you use for analysis and how
... I don't have access to the raw files. I have access to the htseq-count FPKM FPKM-UQ I have read all the questions asked in here. However, I still cannot find a good solution to the following questions 1- I want to find up and down-regulated genes, which package normally do you use ...
rna-seq written 8 hours ago by Learner 80 • updated 4 hours ago by WouterDeCoster24k
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Comment: C: how to proceed in order to find gene regulation
... @jared.andrews07 look above, you can see the example data ...
written 1 day ago by Learner 80
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how to proceed in order to find gene regulation
... I have two questions 1- I have a data which is consists of gene expression values 2- I have data which consists of alternative exon splicing Both data were driven from RNAseq - Now I am trying to find up/down regulated. I read and I found that one uses Dseq2 normally for RNA-seq analysis. Ho ...
genomics rna-seq written 1 day ago by Learner 80
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Comment: C: how can I select WT and Mutated samples
... @Kevin Blighe why would you try to download the raw files? the problem is that the files are controlled so I cannot download them. how can I use this cBioProtal ? do they have all the data that exist in TCGA? In general I am trying to do the following I want to look at the Wild type samples for spec ...
written 2 days ago by Learner 80
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Comment: C: how can I select WT and Mutated samples
... @Kevin Blighe I would like to know if I get the exon for the normal and tumor samples. what are the posibilities to check for differences? for example, do you know a way to check for mutation? or checking the effect of specific genes across two conditions? would you use the gene expression or the F ...
written 3 days ago by Learner 80
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how can I select WT and Mutated samples
... I am trying to download Kidney Renal Rapillary Cell Carcinoma from GDC. I want to know how to extract WT samples (identify which samples are WT) and which samples are mutated samples ? how can I get only those samples ? ...
genome rna-seq written 4 days ago by Learner 80 • updated 4 days ago by Kevin Blighe11k
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finding mutation from RNA seq data
... Hello, I have many samples, I am searching to find whatever package or software which is used for finding mutation using the RNAseq data. I already know about InVex and mutSig . is there any other software or package available? ...
rna-seq written 18 days ago by Learner 80 • updated 18 days ago by Medhat7.3k
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Comment: C: which file to use for analysis
... @Kevin Blighe I have few questions to ask. one is that can you give some definition about your code above? the first lines also I would like to know what you have done for your own newly analysis? did you also check the mutation ? if no, do you know how to find out the mutations across several samp ...
written 19 days ago by Learner 80
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Comment: C: which file to use for analysis
... @Kevin Blighe do you know how to annotate them too? is there any package in python, perl, R or other programing languages ? if you also have any paper, it would help a lot . thanks ...
written 19 days ago by Learner 80

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