Eduardo Gonzalez Grandio

Heatmap overrides precalculated row dendrogram object

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I want to plot the expression of a group of genes (rows) in different conditions (columns), but I want to cluster them based on their sequence similarity, not on their...

Can't find any of the first 10 BED transcript_ids in fasta file

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Hi, I am getting the > Can't find any of the first 10 BED transcript_ids in fasta file error while the transcript_ids of the bed file are clearly in the...

Hello, I plan to use the summit peaks generated by HMMRATAC to study TF binding motifs. In the examples, there is no mention of the need to shift the peak...

Hello, I am trying to generate databases and after downloading, for example, the eggNOGDB, I get the following error: ``` msa2profile /mnt/d/seq_data/tmp/14551941542608933155/msa /mnt/f/seq_data/transannot_dbs/eggNOGDB --match-mode 1 --match-ratio 0.5 --threads 32 -v...

Axes labels are not properly placed when combining faceted and single plots

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I am combinining four plots, two of them have facets and two of them are single plots. They all have the same y axes. When I arrange them, the y...

Inconsistent linewidth in nested facets strips when using strip.background = element_part_rect()

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Hello, I am using the nested facets function and I would like to add a line to better visualize the facet groups using `strip.background = element_part_rect(side = "t")` . However,...

[request] Beeswarm ordered like

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Hello, I wish there was a way of replicating the GraphPad Prism scatter plots in R. Specifically, the "standard" method that preserves the distribution of the datapoints:  Is there...

Add support for [X] cigar string on agat_convert_minimap2_bam2gff.pl

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I am using .bam files created by pbmm2. [This minimap2 wrapper uses the --eqx minimap2 option by default](https://github.com/PacificBiosciences/pbbioconda/issues/217). When I try to convert the .bam file to .gff, I get...

Error obtaining .gfa file with "nextgraph_options = -a 3"

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Hello, I am running NextDenovo with PacBio HiFi reads of a 35 Mb genome. I have been able to produce the fasta file of the assembly but I am getting...

Q: Filtering blacklisted regions when using macs3 hmmeratac

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Hello, I do not see an option to filter out blacklisted regions when using hmmeratac. In the original hmmratac paper they state that this is a crucial step. Should I...