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patrickpflughaupt committed Aug 26, 2024
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Package: kmeRtone
Type: Package
Version: 1.0
Date: 2024-07-17
Date: 2024-08-26
Title: Multi-Purpose and Flexible k-Meric Enrichment Analysis Software
Description: A multi-purpose and flexible k-meric enrichment analysis software.
KmeRtone measures the enrichment of k-mers by comparing the population of
k-mers int he case loci with a carefully devised internal negative control
'kmeRtone' measures the enrichment of k-mers by comparing the population of
k-mers in the case loci with a carefully devised internal negative control
group, consisting of k-mers from regions close to, yet sufficiently distant
from, the case loci to mitigate any potential sequencing bias. This method
effectively captures both the local sequencing variations and broader
sequence influences, while also correcting for potential biases, thereby
ensuring more accurate analysis. The core functionality of KmeRtone is
the SCORE function, which calculates the susceptibility scores for k-mers in
ensuring more accurate analysis. The core functionality of 'kmeRtone' is
the SCORE() function, which calculates the susceptibility scores for k-mers in
case and control regions. Case regions are defined by the genomic coordinates
provided in a file by the user and the control regions can be constructed
relative to the case regions or provided directly. The k-meric susceptibility
scores are calculated by using a one-proportion z-statistic. KmeRtone is
scores are calculated by using a one-proportion z-statistic. 'kmeRtone' is
highly flexible by allowing users to also specify their target k-mer patterns
and quantify the corresponding k-mer enrichment scores in the context of
these patterns, allowing for a more comprehensive approach to understanding
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