Roth E Conrad

Way to get log axes with datashader dsshow and matplotlib

1

#### Is your feature request related to a problem? Please describe. I cannot find a way to get dsshow to return the points with a log axis or convert them...

dsshow savefig error with matplotlib pdf and svg export. Shading intensity variation in png export.

3

#### ALL software version info redhat:enterprise_linux:7.9 Linux 3.10.0-1160.49.1.el7.x86_64 Python 3.8.12 Matplotlib 3.2.2 datashader 0.14.0 pandas 1.1.3 numpy 1.21.6 #### Description of expected behavior and the observed behavior The datashader plotted...

Column labels of the visual output

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Hello, I would like to know what the values of each column are in the visual output and are NA expected for some of the columns? I am seeing: genome1...

I used HiSat2 -dta-cufflinks to assemble 6 separate RNA-seq runs and then Cufflinks version 2.2.1. I am working with A. thaliana data TAIR10 reference genome and annotation files downloaded from...

Missing genes in output after adding alignments to clustering.

2

## Expected Behavior All genes from the input file should be in the output. ## Current Behavior Without adding the alignment the behavior is as expected. But when alignment is...

How are the ID's linked to the Phyla for the phylogenetic tree example?

1

Hey, this looks like a very useful code set. Thanks for your effort here. I would like to customize this for my use, but from the example (without any comments)...

Hello! I hope you are well. simka looks like a great tool! How are the samples normalized with the -max-reads 0 flag? I did not see a description of this...

Core Gene Sweeps phybreak_parameters.txt clarification

2

Hello, I am unclear on the parameter inputs. What is the difference between input_contig_dir and contig_dir and how do these relate to the input genomes dir for PopCOGenT? What are...