User: Vince Schulz

gravatar for Vince Schulz
Vince Schulz60
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v*************@yale.edu

Posts by Vince Schulz

<prev • 12 results • page 1 of 2 • next >
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Comment: C: diffbind dba object subset peak regions
... Thanks. Could you provide clarification on how to generate a new DBA object with a subset of peaks by calling dba() with a mask of peaksets and specify a minOverlap? It seems to me that if I do something like filteredDBA <- dba(originalDBA, mask=somekindofmask, minOverlap=2) then somekindofmas ...
written 3 months ago by Vince Schulz60
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diffbind dba object subset peak regions
... Is it possible to subset peak regions in a dba object with counts prior to differential analysis? In particular, I would like to just analyze regions called in one or more of a subset of samples used for differential analysis in a larger dataset. Other subsetting would be helpful as well, ideally ...
diffbind written 4 months ago by Vince Schulz60 • updated 3 months ago by Rory Stark3.0k
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Diffbind multiple groups
... I have some questions about Diffbind analysis when there are multiple groups to be compared. For example, if we have group1, group2 and group3 and wish to compare group1 vs group2, group1 vs group3 and group2 vs group3. Are all the comparisons fully independent of each other except for the choice ...
diffbind written 9 months ago by Vince Schulz60
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Comment: C: DiffBind MA plot
... The solid blue dots can be removed by adding smoothScatter parameter nrpoints = 0 like dba.plotMA(chipdata, nrpoints = 0) It may be good to make that the default parameter for dba.plotMA. Vince ...
written 17 months ago by Vince Schulz60
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Answer: A: Genomic features for genomic positions
... You may want to look at the annotatePeak function in the ChIPseeker package that does this. Vince ...
written 3.3 years ago by Vince Schulz60
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Comment: C: Genomic features for genomic positions
... You may want to look at the annotatePeak function in the ChIPseeker package that does this.   Vince ...
written 3.3 years ago by Vince Schulz60
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ChIPpeakAnno makeVennDiagram problems
... Hi, I am having problems with ChIPpeakAnno makeVennDiagram problems when the regions of interest do not overlap. This is coming up for me in comparing 4 datasets where two of the datasets don't overlap. It would be great if the function could properly output 0 in the non-overlapping segments. T ...
go bsgenome chippeakanno written 6.6 years ago by Vince Schulz60 • updated 6.5 years ago by Julie Zhu4.1k
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easyRNAseq remove overlapping features
... Hi Nico, I would like to use easyRNAseq to count reads for RNA-seq. The vignette says that "The ideal solution is to provide an annotation object that contains no overlapping features. The disjoin function from the IRanges package off ers a way to achieve this." I do not have much experience with ...
annotation bsgenome iranges easyrnaseq written 6.9 years ago by Vince Schulz60 • updated 6.9 years ago by delhomme@embl.de1.2k
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Answer: A: Mistaken identifiers
... You can prevent the identifiers from being converted by using the excel file import wizard, changing gene name columns from general format to text. You could also try this: #from CRAN library(xlsx) wb <- createWorkbook() sheet <- createSheet(wb, sheetName="CellBlock") datframe <- data.fram ...
written 7.1 years ago by Vince Schulz60
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Motif search -- access to JASPAR, MotIV package, , more TF-PWM relationships?
... In regards to Questions, suggestions, use cases and data sources are all welcome for working with TF-PWM motifs, my 2c: For other methods for de novo chip-seq motif finding besides MotIV and meme, there is a new paper that describes a fast method for chip-seq sets and has recent references: http:// ...
annotation go motiv written 7.6 years ago by Vince Schulz60 • updated 7.6 years ago by Arno BioC10

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For Motif search -- access to JASPAR, MotIV package, , more TF-PWM relationships?

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