User: sarah.blackstone7734

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Posts by sarah.blackstone7734

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Convert HOMER motif matrix to pfm?
... Hi, I have used HOMER to identify a motif for a transcription factor I am studying. Now I would like to load this motif matrix into R and analyze it with bioconductor tools such as PWMEnrich. However, I can not figure out how to convert the HOMER format to .pfm. Has anyone seen a tool, or know how ...
pwmenrich homer written 14 months ago by sarah.blackstone77340 • updated 14 months ago by Ou, Jianhong1000
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Heatmap of motif clusters
... Hi, I am trying to create a similar plot shown on this tutorial:  http://zvfak.blogspot.com/search/label/genomation (under section: Calculating scores that correspond to k-mer or PWM matrix occurence: patternMatrix function). However, I am trying to demonstrate that motifs for different transcri ...
motifs genomation written 14 months ago by sarah.blackstone77340 • updated 14 months ago by altuna akalin10
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ClusterProfiler can't load gmt file
... Hi, I am using clusterProfiler, and I would like to load a collection of gmt files to be used for GSEA. However, the instructions given in the vinette are not working for me.   gmtfile <- system.file("extdata", "genesets.gmt", package="clusterProfiler") c5 <- read.gmt(gmtfile)   I think ...
clusterprofiler gsea gmt written 15 months ago by sarah.blackstone77340 • updated 15 months ago by Guangchuang Yu800
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How to use GRanges to find locations that do NOT overlap?
... I have two GRanges objects, G1 and G2. I would like to subtract the ranges in G2 from G1. findOverlaps(G1,G2) will give me the overlaps, but I want to do the opposite of this. Is it possible? ...
granges written 15 months ago by sarah.blackstone77340 • updated 15 months ago by Michael Lawrence9.8k
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Comment: C: How to change peaks in global matrix in DiffBind?
... Thanks -   I gave it a try, but got an error when running dba.count() > head(cPeaks)   seqnames   start     end 1     chr1 3193392 3193892 2     chr1 4257230 4257730 3     chr1 4332360 4332860 4     chr1 4492080 4492580 5     chr1 4496255 4496755 6     chr1 4560053 4560553 > counts <- db ...
written 15 months ago by sarah.blackstone77340
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How to change peaks in global matrix in DiffBind?
... Hi, I extracted my consensus peakset from the DBA object after counting. I filtered this list to remove outliers and other criteria. I would like to change the consensus peakset in my DBA object now, using my filtered list. I extracted the consensus peaks like this: countTable <- dba.peakset(s ...
diffbind written 15 months ago by sarah.blackstone77340 • updated 14 months ago by Rory Stark2.1k
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DiffBind Analysis with more than 2 samples?
... Hi, I have 2 replicates each of 4 different samples, so 8 samples total (P300 chip-seq). All are from the same cell type, but with different transcription factors knocked out, and also WT. I want to get "modules" of peaks gained and/or lost in each sample (enhancers created or repressed by each T ...
diffbind chip-seq written 15 months ago by sarah.blackstone77340 • updated 15 months ago by Rory Stark2.1k

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