Files in mskilab/loosends
Classifying loose ends in gGraphs
.Rbuildignore
.gitattributes
.github/.gitignore
.github/workflows/check-release.yaml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/bowtie_utils.R
R/build.contigs.R
R/contig.assembly.R
R/contig.support.R
R/contigsupport.R
R/loosends.R
R/loosereads.R
R/pipeline.R
R/telomeres.R
R/utils.R
README.md
inst/extdata/101.unmappable.annotations.rds
inst/extdata/150.unmappable.annotations.rds
inst/extdata/assembly.gaps.ranges.rds
inst/extdata/c.canonical.pdict.rds
inst/extdata/c.noncanonical.pdict.rds
inst/extdata/canonical.telomeres.fa
inst/extdata/g.canonical.pdict.rds
inst/extdata/g.noncanonical.pdict.rds
inst/extdata/noncanonical.telomeres.fa
inst/extdata/reference.sequences.rds
inst/extdata/scripts/loosecalls.R
inst/extdata/scripts/loosereads.R
inst/extdata/telomeres.fa
inst/extdata/tests/loosereads_1/aln.bam
inst/extdata/tests/loosereads_1/aln.bam.bai
inst/extdata/tests/loosereads_1/big.le.dt.rds
inst/extdata/tests/loosereads_1/big.reads.dt.rds
inst/extdata/tests/loosereads_1/le.dt.rds
inst/extdata/tests/loosereads_1/loosereads.bam
inst/extdata/tests/loosereads_1/loosereads.bam.bai
inst/extdata/tests/loosereads_1/loosereads.fq
inst/extdata/tests/loosereads_1/loosereads.res.rds
inst/extdata/tests/loosereads_1/multiple.contig.rds
inst/extdata/tests/loosereads_1/qnames.txt
inst/extdata/tests/loosereads_1/reads.dt.rds
inst/extdata/tests/loosereads_1/single.contig.rds
inst/extdata/tests/loosereads_1/windows.bed
inst/extdata/tests/loosereads_1_normal/aln.bam
inst/extdata/tests/loosereads_1_normal/aln.bam.bai
inst/extdata/tests/loosereads_1_normal/loosereads.bam
inst/extdata/tests/loosereads_1_normal/loosereads.bam.bai
inst/extdata/tests/new_caller_1/dup.aln.rds
inst/extdata/tests/new_caller_1/dup.bp.gr.rds
inst/extdata/tests/new_caller_1/dup.reads.rds
inst/extdata/tests/new_caller_1/dup.seed.rds
inst/extdata/tests/new_caller_1/dup.tigs.rds
inst/extdata/tests/new_caller_1/inv.aln.rds
inst/extdata/tests/new_caller_1/inv.bp.gr.rds
inst/extdata/tests/new_caller_1/inv.reads.rds
inst/extdata/tests/new_caller_1/inv.seed.rds
inst/extdata/tests/new_caller_1/inv.tigs.rds
inst/extdata/tests/new_caller_1/tra.aln.rds
inst/extdata/tests/new_caller_1/tra.bp.gr.rds
inst/extdata/tests/new_caller_1/tra.reads.rds
inst/extdata/tests/new_caller_1/tra.seed.rds
inst/extdata/tests/new_caller_1/tra.tigs.rds
inst/extdata/tests/new_caller_2/cpx.calns.rds
inst/extdata/tests/new_caller_2/del.calns.rds
inst/extdata/tests/new_caller_2/dup.calns.rds
inst/extdata/tests/new_caller_2/fbi.calns.rds
inst/extdata/tests/new_caller_2/inv.calns.rds
inst/extdata/tests/new_caller_2/tra.calns.rds
inst/extdata/tests/new_caller_2/viral.breakends.calns.rds
inst/extdata/tests/pipeline/normal.bam
inst/extdata/tests/pipeline/normal.bam.bai
inst/extdata/tests/pipeline/tumor.bam
inst/extdata/tests/pipeline/tumor.bam.bai
inst/extdata/wide.multimapping.ranges.rds
man/add_contig_ctypes.Rd
man/align_contigs.Rd
man/bowtie_aln.Rd
man/bowtie_index.Rd
man/build_contigs.Rd
man/build_contigs_wrapper.Rd
man/build_pseudo_contigs.Rd
man/call_loose_end2.Rd
man/check_contig_concordance.Rd
man/check_contig_support_wrapper.Rd
man/check_contigs_for_telomeres.Rd
man/check_distal_only_contig_support.Rd
man/check_file.Rd
man/check_split_contig_support.Rd
man/dot-sample.spec2.Rd
man/eighteenmer.Rd
man/find_telomeres.Rd
man/grab_contig_breakends.Rd
man/grab_contig_breakends_wrapper.Rd
man/grab_distal_breakends.Rd
man/grab_looseread_params.Rd
man/grab_loosereads.Rd
man/grab_seed_frame.Rd
man/has_chr.Rd
man/label_contigs.Rd
man/loose.reads2.Rd
man/loosereads_wrapper.Rd
man/minimap_index.Rd
man/munch.Rd
man/parse_realignment.Rd
man/prep_loose_ends.Rd
man/prep_loose_reads.Rd
man/process_loose_ends.Rd
man/qc_contigs.Rd
man/qc_single_contig.Rd
man/read_support.Rd
man/read_support_wrapper.Rd
man/realign_loosereads.Rd
man/seqs_to_fasta.Rd
tests/testthat.R
tests/testthat/test-align_contigs.R
tests/testthat/test-build_contigs.R
tests/testthat/test-contig_assembly.R
tests/testthat/test-contigsupport.R
tests/testthat/test-loosereads.R
tests/testthat/test-new_caller.R
tests/testthat/test-seedframe.R
tests/testthat/test-telomeres.R
tests/testthat/test-utils.R
