inst/CITATION
Ilias Moutsopoulos, Lukas Maischak, Elze Lauzikaite, Sergio A Vasquez Urbina, Eleanor C Williams, Hajk-Georg Drost, Irina I Mohorianu, noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise, Nucleic Acids Research, 2021;, gkab433, https://doi.org/10.1093/nar/gkab433
@Article{,
title = {noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise},
author = {Ilias Moutsopoulos and Lukas Maischak and Elze Lauzikaite and Sergio A. Vasquez-Urbina and Eleanor C. Williams and Hajk-Georg Drost and Irina Mohorianu},
journal = {Nucleic Acids Research},
year = {2021},
month = {06},
abstract = {High-throughput sequencing enables an unprecedented resolution in transcript quantification, at the cost of magnifying the impact of technical noise. The consistent reduction of random background noise to capture functionally meaningful biological signals is still challenging. Intrinsic sequencing variability introducing low-level expression variations can obscure patterns in downstream analyses. We introduce noisyR, a comprehensive noise filter to assess the variation in signal distribution and achieve an optimal information-consistency across replicates and samples; this selection also facilitates meaningful pattern recognition outside the background-noise range. noisyR is applicable to count matrices and sequencing data; it outputs sample-specific signal/noise thresholds and filtered expression matrices. We exemplify the effects of minimizing technical noise on several datasets, across various sequencing assays: coding, non-coding RNAs and interactions, at bulk and single-cell level. An immediate consequence of filtering out noise is the convergence of predictions (differential-expression calls, enrichment analyses and inference of gene regulatory networks) across different approaches.},
issn = {0305-1048},
doi = {10.1093/nar/gkab433},
url = {https://doi.org/10.1093/nar/gkab433},
note = {gkab433},
eprint = {https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkab433/38449279/gkab433.pdf},
}
Ilias Moutsopoulos. Author, maintainer.
Irina Mohorianu. Author, contributor.
Hajk-Georg Drost. Contributor.
Elze Lauzikaite. Contributor.