User: chrisclarkson100

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Posts by chrisclarkson100

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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 8 weeks ago by chrisclarkson10030 • updated 7 weeks 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 10 weeks ago by chrisclarkson10030 • updated 9 weeks ago by shepherl ♦♦ 510
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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 6 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 6 months ago by chrisclarkson10030 • updated 6 months ago by Michael Lawrence9.8k
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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 10 months ago by chrisclarkson10030 • updated 10 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 12 months ago by chrisclarkson10030 • updated 12 months ago by Martin Morgan ♦♦ 20k
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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 14 months ago by chrisclarkson10030 • updated 14 months ago by Peter Langfelder1.3k
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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 15 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 15 months ago by chrisclarkson10030
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converting extremely sparse count dataframe to continuous distributions for study in WGCNA
... I am very inexperienced with mathematics and expression data. I have developed a pipeline for WGCNA, practicing with gene-expression microarray data. I am now determined to try to apply this strategy to microbial-communities count data.  Initially I tried finding an adjacency matrix with the natur ...
voom counts limma voom written 16 months ago by chrisclarkson10030 • updated 15 months ago by Gordon Smyth32k

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