Joshua Kim

Cerealizing a file offset of type `std::streampos`?

4

Hello! I'm trying to serialize a `std::streampos` variable, but am uncertain of how I can do this. If I try and simply archive it, I am told there is no...

Obtaining primary alignment position from secondary alignment?

4

Hello! When it comes to structural variant calling, one characteristic of the presence thereof is a noisier sequence than usual. With these noisy sequences, the secondary alignment can then provide...

Change how seqan3::field::alignment works with SAM/BAM files.

1

Currently, `seqan3::field::alignment` is a default field of SAM/BAM files. However, it requires a reference sequence in addition to the SAM/BAM input (if I'm understanding correctly). For the following case, this...

Computing only binary mappability

4

I think it is oftentimes useful to have a binary mappability of data, when you are only interested in completely unique regions. Up until now, I have been just calculating...

Hello! I came across the following error when trying to visualize a subgraph of a graph with `nk.vizbridges.widgetFromGraph(G)`: ```sh File ~/.local/lib/python3.10/site-packages/networkit/vizbridges.py:188, in widgetFromGraph(G, dimension, nodeScores, nodePartition, nodePalette, showIds, customSize) 185...

Core setup in documentation missing some requirements.

3

Hello! I'm using biocpp core/io for a new project and realized some setup steps seem to be missing/unclear. 1. If I only need the IO module (biocpp-io), I still need...

Sparse to dense coercion when running merge on two Seurat objects.

4

I was trying to create a reproducible example of another issue I'm having with JoinLayers() taking an indefinite amount of time (killed manually after ~12 hours). The dataset I used...

When converting from Seurat RDS to anndata h5ad, gene names are lost.

8

When I convert a Seurat RDS object to h5ad and load the file into a python environment, I see that `object.var_names` is just a list of numbers 1...#_of_genes. Even though...