aleksandrak

oneD normalization

3

Hello, I get the following error while running oneD normalization: Error in formula.character(object, env = baseenv()) : invalid formula "\"tot ~ s(map) + s(cg) + s(res)\"": not a call Calls:...

HIC matrix in .mat format

1

Hello, After generating interaction matrices I have saved them through hic_map function in .mat format. I would like to use the matrices for the downstream analysis, in Python, however I...

TADbit export error

1

Hello, I try to export files using tadbit export and I am getting the follwoing error: tadbit: error: invalid choice: 'export' (choose from 'map', 'parse', 'filter', 'describe', 'clean', 'normalize', 'bin',...

gem-mappability

1

Hello, I am getting the following error, while running gem-mappability on my .gem file Thu Sep 2 23:36:09 2021 -- Loading index (likely to take long)...Fatal error (setup.c:167,input_gem_header) Bad GEM...

I get the following error when running filterPeaks or computeDeviations on my object. Error in Matrix::Matrix(assays(object)$counts) : invalid 'data' Any idea what that could mean? My counts are in matrix...

Is there a way to retrieve/calculate CNV score from CaSpER for bulk data? I have seen other tool calculating log2ratio of reads depth tumor vs normal. Thanks for the help

I am trying to covert my PFMatrixList into PWMatrixList `toPWM(my_PFMatrixList) ` And I get the following error: Error in (function (classes, fdef, mtable) : unable to find an inherited method...

I am comparing enrichment for several different groups. I would like to obtain the list of genes found in each GO term, however when I check greatJob@gene_sets I get the...

I am trying get motifs positions within ATAC-Seq peaks: `motif_ranges sessionInfo() R version 4.3.3 (2024-02-29) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Rocky Linux 9.1 (Blue Onyx) Matrix products: default BLAS/LAPACK: /home/kurowsaa/miniconda3/envs/chromVAR_env/lib/libopenblasp-r0.3.26.so;...

Understanding the scoreType

2

Hello, I am running fgsea on my custom_pathways. I have 445 pathways with rather large gene-sets (see the histogram plot).  Additionally my logFC that I use for ranking the...