chromVAR
chromVAR copied to clipboard
GreenleafLab
chromatin Variability Across Regions (of the genome!)
Hi, I am using Cellranger output to create the SummarizedExperiment object for chromvar. Instead of using the bam/bed file (as it was not working), I used the count and peakranges...
Hi, I have tried some times but not install this successfully yet. Can anyone help me? first, I create a conda environment: `conda create -n r` and then activate r...
Hello, I get the following error when running ``` dev rse class: RangedSummarizedExperiment dim: 4446140 26263 metadata(0): assays(1): counts rownames: NULL rowData names(2): name bias colnames(26263): AAACGAATCGCATACA-1 AAACGAATCGTCCCAT-1 ... TTTGTGTTCCCAGCAG-1...
Nice tool! when using the cisbp to analysis TF enrichment, I found that there are many negative value in the PWM matrix in human_pwms_v2. In this case, I can't plot...
Hello, I would like to know exactly what 'bg_sample_helper' and other functions are doing, but all I found in the code is this: ``` bg_sample_helper
Hello, when I was running `computeDeviations` in the following code, an error occurred: > dev traceback() 17: stop(e) 16: value[[3L]](cond) 15: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14: tryCatchList(expr, classes, parentenv, handlers)...
The above error happens during install of chromVar with BioConductor 3.11 and S4Vectors 0.26.1 elementLengths has been removed from BioC DEPRECATED AND DEFUNCT -- - Remove elementLengths() (was defunct in...
How to convert RangedSummarizedExperiment object to a SummarizedExperiment object?
Hi, Would you recommend using the peaks.bed file in the general outs folder or that in the filtered_peak_bc_matrix sub-folder for chromVAR? Are their advantages to using aggregated peak file vs...
Hi Alicia, How can we retrieve sample specific variability from the Merged chromVar object? If that is not feasible can we compare Variability determined for each sample separately? Thanks
Metadata
Owner
Metadata
chromatin Variability Across Regions (of the genome!)