User: chrisclarkson100

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Posts by chrisclarkson100

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circular genome visualisation: genomic.labels: Error in if (cr != chr) { : missing value where TRUE/FALSE needed
... I am finding your circlize package really useful. However, I am trying to label certain parts of the genome in my circular diagram with the function "genomic.labels" and getting the highlighted error below: library(circlize)   circos.initializeWithIdeogram(chromosome.index = paste0("chr", c(1:22,' ...
genomicfeatures rcircos written 10 weeks ago by chrisclarkson10030
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Error: unable to find an inherited method for function searchSeq for signature matrix
... I am trying to re-implement a script that I found on github (https://github.com/liz-is/ctcf-motif-imr90/blob/master/imr90_ctcf_motif_direction.R). This script finds the directionality of all CTCF sites in IMR90 cells. I would like to use this analysis for mm9 ESC cells. However I have run into a nu ...
tfbstools jaspar pwm written 7 months ago by chrisclarkson10030 • updated 6 months ago by Ge Tan20
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querying annotation hub for common TF, in common cell line returns no results....
... I am trying to query ENCODE for all the datasets it has on CTCF in the mm9 genome. I would have thought that this would be a fairly standard thing but it comes up with no results... hub=Annotationhub() ctcf_imr90 <- query(hub, c("ENCODE","CTCF", "Mus Musculus", "mm9"))   This produces no resu ...
annotate annotationhub written 7 months ago by chrisclarkson10030 • updated 7 months ago by shepherl ♦♦ 560
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Comment: C: trying to annotate overlaps with external file information
... hi thank you- i should have looked through the intersectbed documentation and found out about the -wao option ...
written 11 months ago by chrisclarkson10030
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trying to annotate overlaps with external file information
... I have found the overlapping regions between the genomic regions I am interested in and genes with 'intersectBed'- external of R.  intersectBed -a regions_of_interest.bed -b genes.bed > overlap_genes.bed So now the file looks like this >head overlap_genes.bed chr1 180110925 1801135 ...
iranges granges written 11 months ago by chrisclarkson10030 • updated 11 months ago by Michael Lawrence10.0k
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R memory limit causing problems with genomicRanges operations...
... I have tried, using rtracklayer and Genomicranges to find the overlap between bed files that document different ChIP Seq data e.g. Nucleosome coverage, CTCF coverage etc. I want to then have a csv file that documents the overlapping regions and their occupancy levels e.g. "","seqnames","start","en ...
R bigmemory written 15 months ago by chrisclarkson10030 • updated 15 months ago by theobroma2210
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finding overlapping regions within 2 different bed files with different features
... Is it possible make a file in BED-like format in such a way that each row of data represents a region of the genome and then have different columns to specify the length, the GC content, the DNA methylation, the nucleosome occupancy, Nucleosome Repeat Length and as many features as one could gather, ...
annotation R written 17 months ago by chrisclarkson10030 • updated 17 months ago by Martin Morgan ♦♦ 21k
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WGCNA configured network of low scale-free topology fit
...   I have visually assessed a number of networks configured by WGCNA. The one that I am most happy with however only has a scale-free topology fit of 0.6 R^2. As follows: My downstream analysis of this is to correlate external trait-info to this network: how sure can I be of any inferred correla ...
wgcna written 20 months ago by chrisclarkson10030 • updated 19 months ago by Peter Langfelder1.4k
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displaying network from microbial count data
... I have an abundance table of taxa (columns) and communities (rows). community acanthamoeba acetitomaculum acetivibrio acholeplasma achromobacter 1 AE01 0 0 0 0 1 2 AE02 0 0 0 0 ...
phyloseq written 20 months ago by chrisclarkson10030
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Comment: C: voom for spectral counts
... Here is a related question relating to count data of microbial communities https://support.bioconductor.org/p/85552/ ...
written 21 months ago by chrisclarkson10030

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