User: Alex Gibbs

gravatar for Alex Gibbs
Alex Gibbs40
Reputation:
40
Status:
New User
Location:
Cardiff University
Last seen:
2 months ago
Joined:
3 years, 7 months ago
Email:
g*****@cardiff.ac.uk

I am a first-year PhD student at Cardiff University focusing my studies on the cancer stem cell basis of metastatic skin cancer. KESS2 East Studentship recipient working alongside Skin Care Cymru and Aneurin Bevan University Health Board. I have around 2 years of bioinformatics experience ranging from Microarray and RNA-Seq analysis and R.

Posts by Alex Gibbs

<prev • 11 results • page 1 of 2 • next >
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Query about Z-scores
... Hi everyone! Apologies in advance for the long winded question! Basically, I have been accessing publicly available data in order to shed some light on the relationship between the expression of CD200 (which is a cell surface protein that we are interested in) and cancer prognosis. The other questi ...
rna-seq written 4 months ago by Alex Gibbs40 • updated 11 weeks ago by Biostar ♦♦ 20
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Comment: C: Combining Samples in Microarray Analysis
... Yes, you are correct! I completely forgot about performing group-wise comparisons within Limma, thanks for bringing that up. I will do this instead. ...
written 11 months ago by Alex Gibbs40
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Answer: A: i need to find a database
... You could try using [PubMed's 'Advanced Search'](https://www.ncbi.nlm.nih.gov/pubmed/advanced) a try. All you need to do is plug in the cpg island you are looking for into the search box and then in the dropdown menu to the left, select to search for this cpg island in the title, abstract or all fi ...
written 11 months ago by Alex Gibbs40 • updated 11 months ago by RamRS30k
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Combining Samples in Microarray Analysis
... Hi all, I have 3 disease groups that I would like to compare. Each disease group has 3 samples. Illumina microarray has been performed on each sample along with matched controls. I have generated 9 DEG files for each sample (Affected 1A vs Control, Affected 1B vs Control, Affected 1C vs Control et ...
microarray sequencing written 11 months ago by Alex Gibbs40
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Comment: C: Microarray Heatmap with DEG's
... Thank you very much, Kevin! I will give this a go! ...
written 11 months ago by Alex Gibbs40
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Microarray Heatmap with DEG's
... Hi all! I have generated 18 DEG files which consist of 23,835 genes each (7x Affected_v_Control, 7x Affected_v_Control2, 4x Control_v_Control2). I haven’t filtered these files for Adj.P or LogFC yet. I have then opened these up in Excel and ordered them by probe ID, then taken the LogFC values and ...
R microarray illumina written 11 months ago by Alex Gibbs40 • updated 11 months ago by Kevin Blighe65k
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How to find transcription factor downstream binding
... Hi all, I would like to find out what the mouse Stat3 transcription factor **binds** to and the full signalling pathway(s) that it is involved in. So far, I have only managed to find a signalling pathway that ends in Stat3, and subsequently genes that bind to Stat3. I have tried JASPAR, but the w ...
gene rna-seq written 17 months ago by Alex Gibbs40 • updated 15 months ago by Biostar ♦♦ 20
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GSEA with mouse RNAseq data
... Hi everyone, I have had RNAseq performed on mouse samples (12 samples, 4 groups) and have the results ready to plug into Gene Set Enrichment Analysis (GSEA) software. I notice that there are plenty of human gene sets available on MSigDB, but not many for mouse. I would like to run GSEA with 6 sign ...
rna-seq written 18 months ago by Alex Gibbs40 • updated 12 weeks ago by Gordon Smyth1.9k
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Comment: C: E coli Sequencing & Analysis
... Thank you very much for your reply! I think I will try both methods (SPades&Prokka, NCBI tools) and see which ones I get on with most. ...
written 22 months ago by Alex Gibbs40
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E coli Sequencing & Analysis
... Hello, I have been given the task of assembling a 'new' Ecoli genome and analysing the genes present etc. The Ecoli is a new strain, and has been taken and run on a Nextseq 500 in high-output mode with 150bp paired end reads. The 'raw' files that I have is the forward and reverse reads. I have i ...
genome assembly alignment sequencing written 22 months ago by Alex Gibbs40 • updated 22 months ago by rebeccarenberg20

Latest awards to Alex Gibbs

Popular Question 9 months ago, created a question with more than 1,000 views. For GSEA with mouse RNAseq data
Scholar 11 months ago, created an answer that has been accepted. For A: i need to find a database
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: i need to find a database
Autobiographer 11 months ago, has more than 80 characters in the information field of the user's profile.

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