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/findClusterPartners.R R/hardClust.R R/helperFuctions.R R/import.R R/importReads.R R/plotting.R R/timedMessage.R R/wrapper.R R/wrapper_parallel.R README.md man/EMclust.Rd man/SaaRclust.Rd man/WandCratiosFeatures.Rd man/WminusCratiosFeatures.Rd man/countDirectionalReads.Rd man/countProb.Rd man/countProbOld.Rd man/estimateTheta.Rd man/exportClusteredReads.Rd man/exportGenomicLocations.Rd man/filterInput.Rd man/findClusterPartners.Rd man/findClusterPartners2.Rd man/findClusterPartners_simple.Rd man/findSplitedClusters.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
daewoooo/SaaRclust documentation built on Sept. 30, 2018, 11:21 p.m.