User: Bioinformatist Newbie

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Posts by Bioinformatist Newbie

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Comment: C: Error while invoking. dba.analyze() in DiffBind
... @Rory, It would be much appreciated if you could please help me with the following question: https://www.biostars.org/p/444466/ ...
written 4 months ago by Bioinformatist Newbie250
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Comment: C: DiffBind - Erroneous Affinity Shift In One Direction
... Hi Rory, could you please help me with a question related to dba.contrast available at: https://www.biostars.org/p/444466/ ...
written 4 months ago by Bioinformatist Newbie250
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How to make complex contrasts in DiffBind dba.contrast
... Dear All, I am analyzing ChIP-seq data where I have multiple groups. I am interested in getting differential binding across complex contrasts like: ((condition1 vs. condition2) vs. (condition3 vs. condition4)) **I am unable to figure out how to provide such complex contrast to the `dba.contra ...
R diffbind tool dba.contrast written 4 months ago by Bioinformatist Newbie250 • updated 3 months ago by Rory Stark810
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How to check if there is an association between clustering output (groups) and phenotypic variables (gender, disease stage)
... Dear All, I am interested to know whether there is any association between my clustering groups and phenotypic features (e.g. gender and Braak stages). I have applied spectral clustering on gene expression data from 200 samples (AD and controls) with a fixed number of `clusters = 2`. Ideally, I exp ...
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Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... Hi, thank you for your prompt response. Please note that I have actually tried your given (also above-mentioned) example of custome geneset/pathway creation and finding its enrichment. And I am getting the warning message that I posted in my question, however, I think I should get a table of enrichm ...
written 13 months ago by Bioinformatist Newbie250
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Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... Hello @egeulgen Thank you for providing an interesting and easy-to-follow tutorial. I tried the given script for custom gene set analysis and I am getting the following error, could you please guide me if I am doing something wrong? I am copying-and-pasting the exact code that you shared: ## Te ...
written 13 months ago by Bioinformatist Newbie250
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Comment: C: how to compare two TF binding sites
... If you have peak files for respective TFs and conditions, you can use **Bedtools** [intersect][1] to get what you want. 1a: For overlap binding sites: `bedtools intersect -a TF1.peakFile -b TF2.peakFile > overlappingSites.bed` 1b: For individual binding sites: `bedtools intersect -a TF1.peakF ...
written 2.4 years ago by Bioinformatist Newbie250
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Comment: C: Peak calling with MACS for paired end DNase-seq data
... Thank you for replying. Can you please guide me towards any such reference of using unadjusted pvalue. From unadjusted p-value, do you mean something like `-p 0.5` or so. So that I get more peak but point in this case would be, are those peaks reliable enough? I have got this data from our collabora ...
written 2.5 years ago by Bioinformatist Newbie250
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Comment: C: Peak calling with MACS for paired end DNase-seq data
... Thank you for your suggestion. By trying this: `macs2 callpeak -t MUT1_sorted.bam -f BAMPE -g hs -n MUT1_WT1 -q 0.05 --nomodel --shift 27 --extsize 54` I get only 2574 peaks. I think this number is not reasonable. Let's say if I associate each peak to a gene, even then, only 2574 genes are accessibl ...
written 2.5 years ago by Bioinformatist Newbie250
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Comment: C: Peak calling with MACS for paired end DNase-seq data
... Thank you for replying. I think I am missing many peak regions even if I call peaks without using the control. Please see this [IGV Image][1]. As per my understanding, I should observe a peak for this region as many of the reads are mapping in this region but In actual I don't see a narrow peak for ...
written 2.5 years ago by Bioinformatist Newbie250

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Popular Question 3 months ago, created a question with more than 1,000 views. For How to find Minimum dominating set in a biological network
Great Question 13 months ago, created a question with more than 5,000 views. For Network Comparison by comparing two different adjacency matrices
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Popular Question 2.0 years ago, created a question with more than 1,000 views. For Identify target miRNA for a mRNA
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Popular Question 2.3 years ago, created a question with more than 1,000 views. For Chip-Seq (Transcription Factor) data resources
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Peak calling with MACS for DNase-seq data and Peak annotation by Homer
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How to interpret a heatmap
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