Files in daewoooo/SaaRclust
R Package to cluster long sequencing reads into chromosomes to facilitate de novo genome assembly.
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
R/EMclust.R
R/SaaRclust.R
R/calcProbs.R
R/countDirectionalReads.R
R/dumped_functions.R
R/export.R
R/findClusterPartners.R
R/hardClust.R
R/helperFuctions.R
R/import.R
R/importReads.R
R/plotting.R
R/timedMessage.R
R/utils.R
R/wrapper.R
R/wrapper_parallel.R
README.md
man/EMclust.Rd
man/SaaRclust.Rd
man/WandCratiosFeatures.Rd
man/WminusCratiosFeatures.Rd
man/clusters2ranges.Rd
man/collapseBins.Rd
man/countDirectionalReads.Rd
man/countProb.Rd
man/countProbOld.Rd
man/counts2ranges.Rd
man/estimateTheta.Rd
man/exportClusteredReads.Rd
man/exportGenomicLocations.Rd
man/filterInput.Rd
man/findAntiparallelClusters.Rd
man/findClusterPartners.Rd
man/findClusterPartners2.Rd
man/findClusterPartners_maxMatch.Rd
man/findClusterPartners_simple.Rd
man/findSplitedClusters.Rd
man/flipCounts.Rd
man/gammaFunction.Rd
man/getClusterAcc.Rd
man/getClusterIdentityPerChr.Rd
man/getClusterIdentityPerChrPerDir.Rd
man/getQualMeasure.Rd
man/getRepresentativeAlignments.Rd
man/hardClust.Rd
man/hardClustAccuracy.Rd
man/importBams.Rd
man/importData.Rd
man/importOldTestData.Rd
man/importTestData.Rd
man/kahansum.Rd
man/maxWandCratiosFeatures.Rd
man/mergeClusters.Rd
man/mergeSplitedClusters.Rd
man/plotClustAccuracy.Rd
man/plotHeatmap.Rd
man/plotQualMeasure.Rd
man/plotReadAlignments.Rd
man/plotReadMappingDist.Rd
man/plotThetaEstimates.Rd
man/randomTheta.Rd
man/readBamFileAsGRanges.Rd
man/rescaleTheta.Rd
man/runSaaRclust.Rd
man/thetaRescale.Rd
pipeline/README.md
pipeline/Snakefile
pipeline/processMinimaptab.pl
pipeline/utils/SaaRclust_hardclust_pipeline.R
pipeline/utils/SaaRclust_softclust_pipeline.R
pipeline/utils/install_SaaRclust.R
pipeline/utils/printRead2fasta_pacbio.pl
pipeline/utils/printRead2fastq_strandseq.pl
saarclust_logo.png
utils/Snakefile_plotminimapaccuracy
utils/Snakefile_plotsaarclustresults
utils/minimap_test_outout_accuracy.snakemake.R
utils/minimap_test_plot.snakemake.R
utils/postProcessing.R
utils/processMinimapTest.R
utils/runPostProcessing.R
utils/saarclust_accuracy_plot.snakemake.R
utils/saarclust_cluster_rank_output.snakemake.R
utils/saarclust_cluster_rank_plot.snakemake.R
utils/saarclust_output_accuracy_plot.snakemake.R
utils/saarclust_output_boxplot.snakemake.R
utils/saarclust_plot_boxplot.snakemake.R
vignettes/SaaRclust.Rmd
vignettes/SaaRclust.pdf
