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findGSEP

Accurate estimating genome size is a crucial task in sequencing projects. Current methods often struggle with polyploidy or become inefficient when dealing with species that exceed a ploidy level of six. To address these challenges, we introduce findGSEP, an enhanced version of findGSE. findGSEP utilizes a segmented fitting approach to fit a normal distribution to polyploid species within a segmented framework. This ap-proach simplifies the process of single fitting while significantly expanding the range of ploidy levels it can handle. Moreover, findGSEP offers users interactive tools through both an open-source R application and a web application, facilitating reliable and precise estimation of genome size.

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install.packages('findGSEP')

Monthly Downloads

153

Version

1.2.0

License

GPL (>= 2)

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Maintainer

Laiyi Fu

Last Published

May 26th, 2024

Functions in findGSEP (1.2.0)

kmer_count_modify

Modify K-mer Frequency Before Fitting
initialize_start_time

Initialize Start Time
filter_peaks_raw

Filter Peaks from Raw K-mer Histogram
error_minimize3

Minimize the Error for Remaining K-mer Frequency
error_minimize2_raw

Tuning Final Fitting for Raw Heterozygous Genomes
error_minimize

Minimize the Error for K-mer Frequency Fitting
error_minimize3_raw

Minimize the Error for Raw Remaining K-mer Frequency
findGSEP

Estimate genome size of polyploid species using k-mer frequencies.
findGSE_raw

Estimate Genome Size Using Raw K-mer Frequencies
error_minimize_raw

Minimize the Error for Raw K-mer Frequency Fitting
error_minimize2

Tuning Final Fitting for Heterozygous Genomes
filter_peaks

Filter Peaks from K-mer Histogram
initial_count_recover

Recover Initial K-mer Count
findGSE_sp

Estimate Genome Size Using K-mer Frequencies
initial_count_recover_raw

Recover Initial Raw K-mer Count
get_het_pos

Filter Peaks from K-mer Histogram
kmer_count_modify_raw

Modify Raw K-mer Frequency Before Fitting