Package: findGSEP 1.2.0
findGSEP: Estimate Genome Size of Polyploid Species Using k-Mer Frequencies
Provides tools to estimate the genome size of polyploid species using k-mer frequencies. This package includes functions to process k-mer frequency data and perform genome size estimation by fitting k-mer frequencies with a normal distribution model. It supports handling of complex polyploid genomes and offers various options for customizing the estimation process. The basic method 'findGSE' is detailed in Sun, Hequan, et al. (2018) <doi:10.1093/bioinformatics/btx637>.
Authors:
findGSEP_1.2.0.tar.gz
findGSEP_1.2.0.zip(r-4.5)findGSEP_1.2.0.zip(r-4.4)findGSEP_1.2.0.zip(r-4.3)
findGSEP_1.2.0.tgz(r-4.4-any)findGSEP_1.2.0.tgz(r-4.3-any)
findGSEP_1.2.0.tar.gz(r-4.5-noble)findGSEP_1.2.0.tar.gz(r-4.4-noble)
findGSEP_1.2.0.tgz(r-4.4-emscripten)findGSEP_1.2.0.tgz(r-4.3-emscripten)
findGSEP.pdf |findGSEP.html✨
findGSEP/json (API)
| # Install 'findGSEP' in R: |
| install.packages('findGSEP', repos = c('https://sperfu.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sperfu/findgsep/issues
Last updated 4 months agofrom:8bef3bcce7. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 26 2024 |
| R-4.5-win | NOTE | Oct 26 2024 |
| R-4.5-linux | NOTE | Oct 26 2024 |
| R-4.4-win | NOTE | Oct 26 2024 |
| R-4.4-mac | NOTE | Oct 26 2024 |
| R-4.3-win | NOTE | Oct 26 2024 |
| R-4.3-mac | NOTE | Oct 26 2024 |
Exports:error_minimizeerror_minimize_rawerror_minimize2error_minimize2_rawerror_minimize3error_minimize3_rawfilter_peaksfilter_peaks_rawfindGSE_rawfindGSE_spfindGSEPget_het_posinitial_count_recoverinitial_count_recover_rawinitialize_start_timekmer_count_modifykmer_count_modify_raw
Dependencies:clicolorspacedplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpracmaR6RColorBrewerrlangscalestibbletidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Minimize the Error for K-mer Frequency Fitting | error_minimize |
| Minimize the Error for Raw K-mer Frequency Fitting | error_minimize_raw |
| Tuning Final Fitting for Heterozygous Genomes | error_minimize2 |
| Tuning Final Fitting for Raw Heterozygous Genomes | error_minimize2_raw |
| Minimize the Error for Remaining K-mer Frequency | error_minimize3 |
| Minimize the Error for Raw Remaining K-mer Frequency | error_minimize3_raw |
| Filter Peaks from K-mer Histogram | filter_peaks |
| Filter Peaks from Raw K-mer Histogram | filter_peaks_raw |
| Estimate Genome Size Using Raw K-mer Frequencies | findGSE_raw |
| Estimate Genome Size Using K-mer Frequencies | findGSE_sp |
| Estimate genome size of polyploid species using k-mer frequencies. | findGSEP |
| Filter Peaks from K-mer Histogram | get_het_pos |
| Recover Initial K-mer Count | initial_count_recover |
| Recover Initial Raw K-mer Count | initial_count_recover_raw |
| Initialize Start Time | initialize_start_time |
| Modify K-mer Frequency Before Fitting | kmer_count_modify |
| Modify Raw K-mer Frequency Before Fitting | kmer_count_modify_raw |
