User: reubenmcgregor88

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Posts by reubenmcgregor88

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Colour a phylogenetic tree, based on column in DECIPHER?
... Some background in case I have got the wrong idea here. I have 240 amino acid sequences and want to see how closely related these sequences are (as well as visualising it), and how similar they are between different strains of bacteria. I have a data frame with the sequences as well as a column indi ...
biostrings decipher R written 7 weeks ago by reubenmcgregor880 • updated 7 weeks ago by Erik Wright100
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Comment: C: Is it possible to import a multiple fasta alignemnt (.mfa) file into DECIPHER?
... Thanks Erik, I will look up all the functions individually. on (1) my probelm is there are 175 sequences in one .mfa file. What would be your advice on importing them all in one file? (2) Sorry if I was not clear. I go the steps in slighlty the wrong order, I would like to translate all 175 seque ...
written 9 weeks ago by reubenmcgregor880
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Is it possible to import a multiple fasta alignemnt (.mfa) file into DECIPHER?
... I know this may seem like and obvious question, but I have read the documentation and am finding it hard to destignguish all the different file types etc. I am new to using R for genomics purposes so even an answer potinting me in the right direction of which doumentation to read or tutorials in ter ...
biostrings decipher dna written 9 weeks ago by reubenmcgregor880 • updated 9 weeks ago by Erik Wright100
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Comment: C: Pathway analysis from list of differentially expressed genes with fold change, p
... I have a long list of about 20,000, from an array. Thanks ...
written 3 months ago by reubenmcgregor880
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Pathway analysis from list of differentially expressed genes with fold change, pvalues and normalised expression levels in R
... I have been handed a list of genes from an RNAseq experiment and I have no information about how it was generated as it was done a while ago by a company. I have the lis of genes in columns and pvalues/fold change for different comparisons. I also have the normalised expression values for each gene ...
rnaseq limma R pathway analysis written 3 months ago by reubenmcgregor880 • updated 3 months ago by Lluís R310
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Comment: C: MA plot DiffBind in ggplot2
... Thanks Rory, Related question, in the dba.report() output, what are the column headers named after the conditions (i.e. Conc_condition1, Conc_condition2). I assume these are what is used in the dba.plotMA the bXY=TRUE and are (as you explained above) log2 transformed values, but form where are thes ...
written 5 months ago by reubenmcgregor880
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MA plot DiffBind in ggplot2
... Hi again, sorry lots of questions at the moment, I would like to replicate the following function from diffBind > dba.plotMA(tamoxifen, bXY=TRUE) ​ However I don't know how to retrieve this data, in Deseq2 I believe it would be the baseMean column. Or is the "Conc" column output by "dab.repor ...
chipseq diffbind R ggplot2 written 5 months ago by reubenmcgregor880 • updated 5 months ago by Rory Stark2.3k
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DiffBind broad and narrow peak identification
... Hi,  I have histone, broad-peak data, however some of the peaks are actually rather narrow. So what I can see happening is that the broader peaks are being nicely identified as differentially expressed by diffbind, but the narrow peaks which seem highly up-regulated (with big fold changes) are not ...
chipseq diffbind R written 5 months ago by reubenmcgregor880 • updated 5 months ago by Rory Stark2.3k
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Comment: C: DiffBind consensus peak help
... Ok I have an update, when I switched around my sample sheet (I did this purely as I wanted to have the vitd samples as the positive fold change values) to have the vitd samples at the top, the peak in question is now in the  output of > samples_counts.DB <- dba.report(samples_counts, th=0.1, ...
written 5 months ago by reubenmcgregor880
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Comment: C: DiffBind consensus peak help
... Thanks for this, I learned a bit about the dab.report, Here is my sample sheet: SampleID Tissue Factor Condition Treatment Replicate bamReads ControlID bamControl Peaks PeakCaller                         ...
written 5 months ago by reubenmcgregor880

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