GreenleafLab / chromVAR

chromatin Variability Across Regions (of the genome!)

https://greenleaflab.github.io/chromVAR/

GreenleafLab/chromVAR Issues

Add support for `DelayedMatrix`
Updated 2 months ago
ChromVar installation - Apple silicon - R4.4.1
Updated 3 months ago
chromVAR installation error
Updated 3 months ago3
Use "getBackgroundPeaks" and save bakgrounds as bedfiles rather than indexes
Updated 3 months ago
ChromVAR on integrated dataset - suppressing batch effects ?
Updated 4 months ago
> ggmotif_plot(toPWM(reverseComplement(motifs[[closest_match1]]),type = "prob")) Error in normargPfm(x) : invalid PFM 'x': not an integer matrix
Updated 4 months ago1
computeDeviations group comparison
Updated 4 months ago1
Error in counts_check(object) : ncol(object) > 1
Updated 9 months ago4
Error in counts_check(object) : ncol(object) > 1 is not TRUE
Closed 5 years ago1
Error addGCBias: trying to load regions beyond the boundaries of non-circular sequence "chr13"
Updated 10 months ago1
filterpeaks error
Updated 10 months ago
Error in .local(x, na.rm, dims, ...) : object 'R_dense_rowSums' not found
Updated a year ago1
Issue on chromVAR installation
Updated a year ago1
issue of installing chromVAR
Updated a year ago
Error in get_background_peaks_core(object, bias, niterations, w, bs) : length(bias) == length(fragments_per_peak) is not TRUE
Updated a year ago
Bulk ATAC
Closed 2 years ago
filterPeaks error
Updated 2 years ago
addGCBias Error in value[[3L]](cond) - truncaded file
Updated 2 years ago
Gene name
Updated 2 years ago
Should the repressor really have a negative correlation with its motif?
Closed 2 years ago
chromvar from signac wrapper is stuck (not progressing)
Updated 2 years ago2
Error in chol.default(cov(norm_mat)) :
Updated 3 years ago1
Question about comparing different samples' TF deviation score
Updated 3 years ago
question on background peak selection
Updated 3 years ago
RunChromVAR() error when computing deviations from background
Updated 3 years ago
getCounts error
Updated 3 years ago2
getCounts issue again
Closed 3 years ago
Error filtering the sample
Updated 3 years ago
Cann't install chromVAR successfully on Linux
Updated 3 years ago3
chromVAR computeDeviations error: Error in names(res) <- nms
Updated 3 years ago8
cisbp human_pwms_v2
Updated 4 years ago
Question: How to see the code of functions like '_chromVAR_bg_sample_helper' ?
Updated 4 years ago
chromVAR computeDeviations error:Error in isVirtualExt(exti) :
Updated 4 years ago5
Error: object 'elementLengths' is not exported by 'namespace:S4Vectors'
Updated 4 years ago
createArrowFiles function
Closed 4 years ago
How to convert RangedSummarizedExperiment object to a SummarizedExperiment object?
Updated 4 years ago
How to convert RangedSummarizedExperiment object to a SummarizedExperiment object?
Closed 4 years ago
Choice of Peak files to use in chromVAR analysis
Updated 4 years ago2
Merged chromVAR analysis Question
Updated 4 years ago
Generating a Variability Plot of a handful of motifs
Updated 4 years ago
could not find function ".validate_Vector_vertical_slots"
Closed 4 years ago4
[feature-request] variable-width peaks in chromvar
Updated 4 years ago
Error message when running matchMotifs() function
Updated 5 years ago
Normalization steps when merging different samples in chromVAR
Updated 5 years ago
Adding motifs to JASPAR2018
Closed 5 years ago
no output
Updated 5 years ago
Issue plotting Heatmap
Updated 5 years ago
any other genome
Updated 5 years ago
Advice for cases when correcting deviations for metadata is needed
Updated 5 years ago
how to "Using your own matrix of fragment counts" with depth
Updated 5 years ago