Cedric Laczny

This is a "foward" from https://github.com/RGLab/Rtsne.multicore/issues/7 # Part 1 I observed that the results differ based on the number of threads specified. In my application which used BH-SNE to create...

Hi, first of all, thank you for developing the software! I ran it on some samples that were sequenced with a NextSeq 2000. For some samples, the reads are mostly...

When visualizing sequences that are derived from a larger collection (say, 20) of labels, the symbols for "circle" and for "rectangle" are not consistent between the legend and the main...

Problems in polygonal selection with very deep zooming

1

When zooming in deeply and doing a polygonal selection it seems that the decision if a point belongs to a cluster (`contains()`) becomes problematic: ![screen shot 2014-12-02 at 08 13...

The user can pretty much provide any file as input, even it is not a FASTA file. This should be checked more stringently and communicated to the user.

Currently, the `DataSetFactory` normalizes the GC and coverage values of a `Sequence` with respect to the maximum in the `DataSet`. However, this should **not** be done in this way. The...

Currently, VizBin stores the FASTA sequences in memory. This typically works well for current (i.e., short read-based, say Illumina) metagenomic assembly results. However, third-generation sequencing (e.g., PacBio, ONT) may result...

Allowing to specify input files at the command-line

13

It would be nice to have a way to run VizBin in "non-interactive" mode. That means that the user should be able to set the values of the individual fields...

Update the wiki

1

The wiki needs update.

VizBin has evolved organically over time and has multiple contributing authors. The underlying Java code could thus benefit from a rewrite, at least by the increased use of existing Java...