What the package does (short line)

Global functions | |
---|---|

ann_check_nccontig | Source code |

ann_contig_to_adjmat | Source code |

assemble | Source code |

assemble.core | Source code |

assemble.core.recode | Source code |

assemble.trim.centroid | Source code |

assemble.trim.centroid.core | Source code |

assemble_centroid | Source code |

assign.reads.to.centroids | Source code |

binom.bf | Source code |

bmf | Source code |

cal.dist | Source code |

cal.logLR | Source code |

cal.logLR.H0 | Source code |

cal.logLR.H1 | Source code |

cal.nlogn | Source code |

calCondFreq | Source code |

calLinkDist | Source code |

check.contain | Source code |

check.m5 | Source code |

check_contained_reads | Source code |

check_link_loci | Source code |

cluster.knn | Source code |

const.haplotype | Source code |

conv_encode_to_mat | Source code |

correct.reads | Source code |

countfreq | Source code |

cutwindow | Source code |

decode.snv | Source code |

detect.multiple | Source code |

detect.single | Source code |

detect.single.legacy | Source code |

dforest_link_loci_olc | Source code |

dist_hamming | Source code |

encode.snp | Source code |

eval.ann | Source code |

eval.ann.legacy | Source code |

eval.centroid | Source code |

eval.consensus | Source code |

filter_pileup_var | Source code |

findReadsByLoci | Source code |

find_read_pairs | Source code |

get.depth | Source code |

get.depth.samtools | Source code |

get.haplo.seq | Source code |

get.movie | Source code |

getReadsByID | Source code |

getVarComb | Source code |

get_cons_bymovie | Source code |

get_consensus | Source code |

get_consensus_recode | Source code |

get_nccontig | Source code |

getsnpmat | Source code |

kmeans_reads | Source code |

kmeans_reads_core | Source code |

link.scafold | Source code |

link.scafold.bak | Source code |

load.annfile | Source code |

load.cmpreadsfile | Source code |

load.dist | Source code |

load.encodefile | Source code |

load.jaccardfile | Source code |

load.m4file | Source code |

load.m5file | Source code |

load.output | Source code |

load.snp.code | Source code |

load.testfile | Source code |

load.varfile | Source code |

mat_fac | Source code |

mat_fac_long_reads_first | Source code |

mat_fac_mindist | Source code |

mat_fac_old | Source code |

mat_fac_rank_1 | Source code |

mat_fac_rank_1_core | Source code |

mat_fac_rm_redudant | Source code |

merge.scafold | Source code |

merge.scafold.core | Source code |

merge.scafold.extend | Source code |

merge.scafold.extend.core | Source code |

merge_centroid | Source code |

mix.m5 | Source code |

mod.cluster | Source code |

mod.cluster.core | Source code |

mod.cluster.sub | Source code |

olc | Source code |

parse.cigar | Source code |

parse.nucmer | Source code |

parse.snp | Source code |

pileup_reads | Source code |

pileup_reads_count | Source code |

pileup_var | Source code |

pileup_var_count | Source code |

pileup_var_count_recode | Source code |

plot.encode.data | Source code |

prefix_tree_cluster | Source code |

print_pileup | Source code |

read.context | Source code |

read.pileup | Source code |

read.similarity | Source code |

read.similarity.core | Source code |

reads.to.graph | Source code |

rm.isolated.nodes | Source code |

sample.reads | Source code |

save.encodefile | Source code |

save.m5file | Source code |

sclust | Source code |

sim_jaccard | Source code |

slide_win_clustering_core | Source code |

summary | Source code |

trim.m5 | Source code |

trim_centroid | Source code |

unconvolve.scafold | Source code |

validate.data | Source code |

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