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Zarr vs HDF5: First benchmarks & impact of chunk size

About chunks

Like HDF5, the Zarr format stores the array data in physical chunks:

• Chunks are typically small rectangular regions of the array (e.g. 100x100).

• They span the full array with no overlaps (tiles).

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Introduction

The WGXG and FGXG motifs

The FWR4 region in a germline J gene allele is expected to start with amino acid motif WGXG on the heavy chain and FGXG on the light chain. Note that X represents any amino acid.

However, we've found that some of the germline J gene alleles provided by IMGT or AIRR-community/OGRDB do not conform to this.

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How can we make some matrix operations more efficient in Bioconductor

Goal: can we efficiently perform a single-cell analysis fully in memory, even for a big dataset like the 1.3M cells dataset? As long as the machine has enough memory.

Here are some low-hanging fruits that have the potential to significantly improve the current situation.

Role of the SparseArray package

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BLAS benchmarks

WORK IN PROGRESS!

1. The operations that we benchmarked

We benchmarked the following operations (all operations got timed with system.time()):