User: jason.williams

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Posts by jason.williams

<prev • 11 results • page 1 of 2 • next >
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transcriptR predictStrand Error: subscript contains invalid names
... Hi, I am following this vignette for transcriptR (https://bioconductor.org/packages/release/bioc/vignettes/transcriptR/inst/doc/transcriptR.pdf) an R package that combines RNA-seq and ChIP-seq data. The predictStrand feature combines the data contained within the RNA-seq and ChIP-seq data objects c ...
transcriptr predictstrand written 4 weeks ago by jason.williams0
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Comment: C: transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
... Thanks James. I did suspect this was the case, but thank you for confirming,I have to wait for permission to load the hg38.knownGene library. I will be able to do this next week. So yes, I will choose B! High risk of diabetes type I 8| although any reference genome should only be used for alignment ...
written 5 weeks ago by jason.williams0
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Comment: C: transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
... Hi James. I have edited it now. The preview actually wasn't the same as what was being posted. When I removed the code chunk title, the post became the same as the preview. ...
written 5 weeks ago by jason.williams0
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transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
... Hi, I'm following this vignette (https://rdrr.io/bioc/transcriptR/f/vignettes/transcriptR.Rmd) for transcriptR, when estimating gap distance I get the following error. ``` # create a range of gap distances to test # from 0 bp to 10000 bp with the step of 100 bp gd <- seq(from = 0, to = 10000, b ...
rna-seq chip-seq transcriptr written 5 weeks ago by jason.williams0 • updated 5 weeks ago by James W. MacDonald52k
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Comment: C: Cannot put file path in for bam file when attempting to construct a TDS in trans
... Hi James, I apologise for this, I failed to load the transcriptR library like you said. This was not helped by the fact that this library is not loaded in the vignette, also I did not have permission to install the package in the docker I am operating in! But I will stop making excuses. Thank you f ...
written 5 weeks ago by jason.williams0
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Comment: C: Cannot put file path in for bam file when attempting to construct a TDS in trans
... Thank you so much James. I am able to put the file path in now, but even after loading the packages it still cannot find the constructTDS function: ``` > if (!requireNamespace("BiocManager", quietly=TRUE)) + + if (!requireNamespace("BiocManager", quietly=TRUE)) + install.packages("BiocManager" ...
written 6 weeks ago by jason.williams0 • updated 6 weeks ago by James W. MacDonald52k
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Comment: C: Cannot put file path in for bam file when attempting to construct a TDS in trans
... Hi James, Thanks for your help. Here's the whole code from the r markdown I started to make. title: "trasncriptR" author: "Jason" date: "17/10/2019" output: html_document --- ```{r download transcriptR} if (!requireNamespace("BiocManager", quietly=TRUE))+ ins ...
written 6 weeks ago by jason.williams0 • updated 6 weeks ago by Martin Morgan ♦♦ 24k
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Cannot put file path in for bam file when attempting to construct a TDS in transcriptR
... Hi, I am following this vignette to use transcriptR to combine RNASeq and ChIPSeq data. https://bioconductor.org/packages/release/bioc/vignettes/transcriptR/inst/doc/transcriptR.pdf Unfortunately I'm falling at the first hurdle - as when I am trying to insert the path to bam file for my RNASeq f ...
transcriptr written 7 weeks ago by jason.williams0 • updated 7 weeks ago by James W. MacDonald52k
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Comment: C: Using tximport on rsem files produces error while trying to read in files
... Hi ,I have this length(files) > 0 is not TRUE. I don't understand this last response. I paste my code here, could you let me know if you have any idea how to fix this: ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("tximport") lib ...
written 3 months ago by jason.williams0 • updated 3 months ago by Michael Love26k
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Comment: C: unknown error in DiffBind package
... HI both, I have the same problem as Roberta. My bam.bai files are in the same folder as my bam alignments. I ran the following script: library("DiffBind") # read csv of sample sheet into dataframe samples <-read.csv(Extreme_Phenotype_H3K27Ac.csv) samples # Load and read the sample sheet DBdata ...
written 4 months ago by jason.williams0

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