User: fawazfebin

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fawazfebin100
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Posts by fawazfebin

<prev • 39 results • page 1 of 4 • next >
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Comment: C: RMA normalisation for Illumina micro array data
... Thanks, I shall check out. ...
written 12 weeks ago by fawazfebin100
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RMA normalisation for Illumina micro array data
... Hi, I need to normalize some transcriptomic data obtained from GEO using RMA algorithm. The experiment was performed using Illumina HumanHT-12 V4.0 expression beadchip. I am unable to get a proper package/code for the same. Can anyone please guide? Thanks in advance! Febin ...
geo illumina micro array normalisation R written 12 weeks ago by fawazfebin100
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Reference sequence for miRNA-Seq differential expression analysis
... Hi I am doing a differential expression analysis on miRSeq data. Since the reference miRNA sequence was not available in miRBase, I need to download them from a different database, PmiREN. I am confused on which miRNA reference sequences are to be downloaded to perform mapping using mirDeep2. Here ...
mirna-seq mirdeep2 differential expression written 4 months ago by fawazfebin100 • updated 4 months ago by _r_am32k
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Comment: C: What is an OTU?
... Greatly appreciating the clarification! ...
written 6 months ago by fawazfebin100
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Answer: A: What is an OTU?
... In metagenomics, OTU or Operatinal Taxonomic Unit is used to classify bacteria based on sequence similarity of the 16S marker gene. An OTU consists of a group of bacteria whose 16S marker gene shows a sequence identity of 97 percent and above. It is used to classify bacteria at the genus level. ...
written 6 months ago by fawazfebin100
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Developing machine learning models from protein-ligand interactions
... Hi Suppose that after screening libraries of drug molecules, I have a list of active compounds that docks into the protein. Is it possible to develop a machine learning model for those compounds that have the desired activity? Where can I get the guidance for the same? I would really appreciate ...
docking protein machine learning ligand written 7 months ago by fawazfebin100
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Comment: C: removing decimal from ENSEMBL gene ID from deseq2 output
... How would you alter the command if there are two digits after the decimal point, say ENSG00000000460.15 ? I am not able to remove the numbers after the decimal point in such cases using the above command. ...
written 9 months ago by fawazfebin100
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Comment: C: removing decimal from ENSEMBL gene ID from deseq2 output
... How would you alter the command if there are two digits after the decimal point, say ENSG00000000460.15 ? I am not able to remove the numbers after the decimal point in such cases using the above command. ...
written 9 months ago by fawazfebin100
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Answer: A: Drug resistant vs. Drug sensitive data retreival from TCGA
... Hi @Chaimaa I used both of the columns for categorisation. Cases with ' new_tumor_event_indicator' as 'YES' & tumor_status' as 'WITH TUMOR' were grouped as 'resistant'. The sensitive cases would correspond to the absence of new tumor event & tumor free status. R commands are available to s ...
written 9 months ago by fawazfebin100
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Comment: C: Drug resistant vs. Drug sensitive data retreival from TCGA
... Under the 'Clinical' files you can find different .txt files which gives you information about the drug used (clinical_drug .txt file) and disease recurrence ( follow_up .txt file). The 'new_tumor_event' cases can be grouped as 'resistant' and the cases without a 'new_tumor_event' and that are 'tumo ...
written 10 months ago by fawazfebin100

Latest awards to fawazfebin

Supporter 12 weeks ago, voted at least 25 times.
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: What is an OTU?
Appreciated 6 months ago, created a post with more than 5 votes. For A: What is an OTU?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What is an OTU?
Popular Question 16 months ago, created a question with more than 1,000 views. For Access of triple negative breast cancer datasets from GDC
Popular Question 17 months ago, created a question with more than 1,000 views. For Access of triple negative breast cancer datasets from GDC

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