User: phil.chapman

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phil.chapman140
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p***********@cruk.manchester.ac.uk

I am Lead Scientist for Bioinformatics in the Drug Discovery Unit at the Cancer Research UK Manchester Institute. 

Posts by phil.chapman

<prev • 23 results • page 2 of 3 • next >
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Answer: A: RNAseq reads mapped to the gene
... Since featureCounts gives you a matrix of reads counts with genomic feature as the row name and sample as the column name, you can calculate the number of reads that have been mapped to the features defined in your annotation by calculating the sum of your matrix. fc <- featureCounts(files=bam_ ...
written 2.4 years ago by phil.chapman140
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Answer: A: Getting gene ID's from camera results
... Since these are MSigDB gene set collections you could just use the .gmt files directly or one of a number of bioconductor packages that can process these for you.  I use the piano package quite a lot which has a loadGSC function, so having downloaded, for example, the hallmarks .gmt file (h.all.v5.0 ...
written 2.4 years ago by phil.chapman140
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Answer: A: Updated DESeq2 performance on highly replicated yeast RNA-seq data
... Mike, This is a really useful analysis and dataset, but it is just a single dataset.  How might you anticipate the results differing in a system with more or less biological variability?  The work I do tends to involve treating cancer cell lines with novel compounds, so there is really very little ...
written 2.5 years ago by phil.chapman140
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Tutorial: Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
... We've just been trialling the Lexogen Quantseq 3'-UTR RNAseq protocol and I thought I'd share the write-up I put together in case anyone else finds it useful.  I really valued being able to do this all in Bioconductor since I wasn't having to swap environments all the time to use different tools and ...
shortread rsubread tutorial ensembldb written 2.5 years ago by phil.chapman140
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Answer: A: Missing the package called 'R.oo'. Please help me to fix, thanks.
... Have you tried installing the R.oo package from CRAN using: install.packages('R.oo' ) https://cran.r-project.org/web/packages/R.oo/index.html ...
written 2.5 years ago by phil.chapman140
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Answer: A: LuminalA Breast cancer subtype samples from GEO GSE62944
... Not sure how to do it in Bioconductor but the cgdsr package (from CRAN) that accompanies the cBio Portal has some useful pre-defined sets of cases that relate to different breast cancer subtypes.  I think that these have been manually curated from the original publication.  Anyway, take a look at th ...
written 2.5 years ago by phil.chapman140
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Comment: C: ShortRead quality assessment functions (qa and qa2) from ShortReadQ object
... Great thanks for the clarification and hints Martin. ...
written 2.5 years ago by phil.chapman140
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ShortRead quality assessment functions (qa and qa2) from ShortReadQ object
... Hi, Is it possible to use the ShortRead::qa2() function from a ShortReadQ object rather than a fastq file?  I'm doing various trimming and manipulation using ShortRead so since the data is in memory, I don't want to write it out to read it back in again.  This is possible with qa() but for  qa2 I c ...
shortread written 2.5 years ago by phil.chapman140 • updated 2.5 years ago by Martin Morgan ♦♦ 22k
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Comment: C: Using ShortRead (or other) to trim from pattern match onwards
... Hi Martin, Just an example with timings to show what happens when the ByPos_MIndex start method gets called.  Again the start point is example(trimEnds).  I can see that the start method for a ByPos_MIndex object is derived from that from a RangesList object which in turn uses an lapply so presumab ...
written 2.5 years ago by phil.chapman140
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Comment: C: European Bioconductor Developers Meeting: Cambridge 7/8th December 2015
... Thanks for the information Mark and Mike.  I'm already attending the Wellcome Trust Target Validation and Informatics conference at Hinxton from Tuesday lunch to Thursday evening so was just looking to tie it in with that really.  Travelling from CRUK Manchester so just trying to work out if I'd hav ...
written 3.0 years ago by phil.chapman140

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Autobiographer 2.4 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 2.5 years ago, created an answer that has been accepted. For A: Meta analysis of healthy and diseased data using illumina microarrays

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