Computational artifacts (preprint)

derfinder : Software for annotation - agnostic RNA - seq differential expression analysis

Background Differential expression analysis of RNA sequencing (RNA-seq) data typically relies on reconstructing transcripts or counting reads that overlap known gene structures. Previously we introduced an intermediate approach called differentially expressed region (DER) finder that seeks to identify contiguous regions of the genome showing differential expression signal at single base resolut...

Bartender: an ultrafast and accurate clustering algorithm to count barcode and amplicon reads

Barcode sequencing (bar-seq) is a high-throughput, and cost effective method to assay large numbers of lineages or genotypes in complex cell pools. Because of its advantages, applications for bar-seq are quickly growing – from using neutral random barcodes to study the evolution of microbes or cancer, to using pseudo-barcodes, such as shRNAs, sgRNAs, or transposon insertion libraries, to simult...

UHasselt Computational Mathematics Preprint Series

Dealing with Boundary Artifacts in MCMC-Based Deconvolution

Many numerical methods for deconvolution problems are designed to take advantage of the computational efficiency of spectral methods, but classical approaches to spectral techniques require particular conditions be applied uniformly across all boundaries of the signal. These boundary conditions– traditionally periodic, Dirichlet, Neumann, or related–are essentially methods for generating data v...

Lapped biorthogonal transforms for transform coding with reduced blocking and ringing artifacts

Two new lapped transforms are introduced: the LBT (lapped biorthogonal transform) and the HLBT (hierarchical lapped biorthogonal transform). The LBT has the same computational complexity of the LOT (lapped orthogonal transform), with much less blocking artifacts. The HLBT has a significantly lower computational complexity than the LOT, essentially no blocking artifacts, and less ringing artifac...