API for zhixingfeng/rGDA
What the package does (short line)
| Global functions | |
|---|---|
| ann.reconsensus | Source code |
| ann.reconsensus.bak | Source code |
| ann_check_nccontig | Source code |
| ann_contig_to_adjmat | Source code |
| ann_to_graph | Source code |
| ann_to_graph.legacy | Source code |
| assemble | Source code |
| assemble.core | 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 |
| binom_log_bf_bayes | 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 |
| calCondFreqRef | Source code |
| calLinkDist | Source code |
| check.ann | 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 |
| context.effect.encode | Source code |
| context.effect.learn.cv | Source code |
| context.encode | Source code |
| conv_encode_to_mat | Source code |
| correct.reads | Source code |
| correct_contig | Source code |
| correct_reads_jaccard | Source code |
| correct_reads_maxlen | 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 |
| estBetaParams | Source code |
| eval.ann | Source code |
| eval.ann.coverage | Source code |
| eval.ann.hamming | Source code |
| eval.ann.heatmap | Source code |
| eval.centroid | Source code |
| eval.consensus | Source code |
| eval.detection | 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_consensus_recode_legacy | Source code |
| get_consensus_recode_recap | Source code |
| get_nccontig | Source code |
| get_sig_contigs | Source code |
| getsambyname | Source code |
| getsnpmat | Source code |
| interval_union | 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.dforestfile | Source code |
| load.dist | Source code |
| load.encodefile | Source code |
| load.jaccardfile | Source code |
| load.m4file | Source code |
| load.m5file | Source code |
| load.m5qvfile | Source code |
| load.output | Source code |
| load.pu.qv.file | Source code |
| load.pu.qvc.file | Source code |
| load.snp.code | Source code |
| load.testfile | Source code |
| load.upath | 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 |
| merge_encode | Source code |
| mix.m5 | Source code |
| mod.cluster | Source code |
| mod.cluster.core | Source code |
| mod.cluster.sub | Source code |
| olc | Source code |
| pair_jaccard | Source code |
| parse.cigar | Source code |
| permute.reads | 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 |
| pileup_var_count_recode_pairwise | 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.annfile | Source code |
| save.encodefile | Source code |
| save.m5file | Source code |
| sclust | Source code |
| sim_jaccard | Source code |
| sim_jaccard_pairwise | Source code |
| slide_win_clustering_core | Source code |
| split.ann.by.group | Source code |
| summary | Source code |
| test_contig | Source code |
| test_contig_pair | Source code |
| test_contig_pair_legacy | Source code |
| test_contig_pairwise | Source code |
| trim.m5 | Source code |
| trim_centroid | Source code |
| unconvolve.scafold | Source code |
| validate.data | Source code |
| xgboost.cv | Source code |
