User: Bioinformatician_in_trouble

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Posts by Bioinformatician_in_trouble

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Python Code to standardize gene name in CSV file
... I can use regex for symbols. But in general i would want to replace all gene names as is given in HGNC. PD-L1 was just an example. ...
written 14 days ago by Bioinformatician_in_trouble0
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Comment: C: Python Code to standardize gene name in CSV file
... Yes, HGNC symbols. For example: My CSV file may have "TS" as an input but HGNC symbol for that is TYMS. So, I want TYMS as output. But I do not want to replace each gene symbol manually. Species is Human and the genes names are coming from Pubmed abstracts( so different authors refer genes different ...
written 14 days ago by Bioinformatician_in_trouble0
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Python Code to standardize gene name in CSV file
... Hi all, I have a CSV file that includes gene names in different formats for example: PD-L1 might be written as PDL1 or PD-L1 or PDL-1 but i want to standardize all of these to HGNC symbols using python code. Can anyone tell me how should I go about it. I know how to do it for just one gene name ( i ...
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Comment: C: Coloring nodes according to attribute value in Cytoscape 3
... Sorry for late reply.Thank you so much. ...
written 14 days ago by Bioinformatician_in_trouble0
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Comment: C: Coloring nodes according to attribute value in Cytoscape 3
... hi i have the same issue. How did you solve the problem? ...
written 5 weeks ago by Bioinformatician_in_trouble0
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Comment: C: Cytoscape: how to show different interactions using different lines or different
... Hi asaf, Thank you for your reply.I am not sure how to add attributes( saw the attribute file format from cytoscape manual, but could not follow) This is how i have placed the columns in the excel sheet that I used to create network Gene 1 Gene 2 Interaction ATM TP53 Activates CHEK1 CDC25 Inhibits ...
written 5 weeks ago by Bioinformatician_in_trouble0
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Cytoscape: how to show different interactions using different lines or different colors
... Hi All, I am trying to create a network in cytoscape 3.4.0 where my source and target are genes and my interaction would be "activates" or "Inhibits". My question is, I want to show the interactions either by using different line color or different line type. How can I do this. ? Looking forward for ...
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Comment: C: Detection of fusion from a DNA seq file
... Organism: Human I know the genes that are fused. I have a BAM file that contains the DNA sequence. I tried running TOPHAT fusion but it gave zero fusions. I am not sure how to run Breakdancer, as the perl and cpp version is confusing for me, even after reading the tutorial. TIA. ...
written 6 weeks ago by Bioinformatician_in_trouble0
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Detection of fusion from a DNA seq file
... Hi, Can anyone please suggest some free softwares that could help in detection of fusion from a DNA seq file.? Looking forward for response. Thank you in advance. ...
next-gen written 6 weeks ago by Bioinformatician_in_trouble0 • updated 6 weeks ago by Etal1.6k
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Comment: A: MPile up Result contains "X" in Alt column
... Thank you both of you for your reply. @ Devon Ryan: It is a local instance of galaxy. And My output from mpileup is a VCF file, so I am not sure how useful will Bcftools will be. @ Berge2015 :Thank you,I did see these posts.But again,it was on command line. And I am using the web version of galaxy. ...
written 5 months ago by Bioinformatician_in_trouble0

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