chromVAR

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matchKmers does not sample all permutations

1

When using `matchKmers(6,counts_filtered, genome=BSgenome.Mmusculus.UCSC.mm10)` the function runs successfully but does return only matches for 2080 sequences. Comparinson to a set off all 4096 6mers does not show any systematic scheme...

arendma

statistical test for p-value

1

Hi Alicia, Could you please let me know the name of the statistical test performed in the computeVariability function? Am I correct that it is a Brown-Forsythe test? Thanks for...

agehrke6

Question: Where is register(MulticoreParam(8)) being used

1

I was wondering where in chromVAR parallel processing was being used. In the vignette it is stated to set ``` library(BiocParallel) register(MulticoreParam(8)) ``` but in digging through the code I...

stephenwilliams22

Hi, could ChromVAR be applied to two ATAC-seq sample from two plant tissues (like leaf and flower, not single cells)? If it could, is there any parameters that I should...

airichli

De novo motif

1

Hi, I am trying to compute de novo motif and the routine returns 0 de novo motifs. Any idea how can I troubleshoot the routine? Thanks

marianogabitto

getCounts Error

3

Greetings to you. I have been trying to use the getCounts function in chromVAR. Unfortunately, the script always ends up with the following error message: "Error in validObject(.Object) : invalid...

chadi-elfarran

readNarrowpeaks() parsing failure

1

Hi, in the current chromVAR version (1.2.0) the function `readNarrowpeaks()` creates a parsing error, depending on the chromosome naming scheme and the amount of peaks. This is caused by the...

TobiTekath

Normalization for bulk ATAC-seq

1

I have bulk ATAC-seq from two cell populations (two replicates each). Papers suggest for bulk counts to apply quantile normalization followed by GC bias normalization using CQN. Does chromVAR account...

ma-ta-ta

The effect of running computeDeviations without Deviations

1

If I run `computeDeviations` on a chromVARCounts object without providing annotations, then I expect the deviations thus computed are the chromatin accessibilities of the input peaks. But is it safe...

JohnMCMa

Peaks without overlapping reads

1

Hi, When doing downstream analysis we remove cells that we do not trust, and after resizing this can result in peaks without any overlapping reads. It seems that chromVAR does...

timydaley