Files in TRON-Bioinformatics/splice2neo
Aberrant splice junction analysis with associated mutations
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
.gitlab-ci.yml
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/add_context_seq.R
R/add_peptide.R
R/add_tx.R
R/annotate_mut_effect.R
R/bed_to_junc.R
R/canonical_junctions.R
R/choose_tx.R
R/combine_mut_junc.R
R/data.R
R/define_junc_id.R
R/easyquant.R
R/exon_in_intron.R
R/format_pangolin.R
R/format_spliceai.R
R/get_junc_pos.R
R/globals.R
R/is_canonical.R
R/is_in_rnaseq.R
R/junc_to_gr.R
R/leafcutter_parsing.R
R/mmsplice.R
R/modify_tx.R
R/parse_gtf.R
R/parse_pangolin.R
R/parse_spliceai.R
R/spladder_parsing.R
R/standardize_junctions_RNA_tools.R
R/unique_mut_junc.R
R/utils-pipe.R
README.Rmd
README.md
_pkgdown.yml
codecov.yml
data-raw/build_pangolin_example.sh
data-raw/canonical_example.feather
data-raw/toy_transcripts.R
data/canonical_juncs.rda
data/toy_cds.rda
data/toy_junc_df.rda
data/toy_junc_id.rda
data/toy_junc_id_enst.rda
data/toy_transcripts.rda
data/toy_transcripts_gr.rda
data/unsorted_junc_df.rda
inst/CITATION
inst/WORDLIST
inst/extdata/example/MMsplice.csv
inst/extdata/example/easyquant/quantification.tsv
inst/extdata/example/gencode.v34lift37.annotation.subset.gtf.gz
inst/extdata/example/gene_table.tsv
inst/extdata/example/leafcutter/Leafcutter.perind.counts.gz
inst/extdata/example/regions.tsv
inst/extdata/example/spladder/sample_alt_3prime_C3.confirmed.txt.gz
inst/extdata/example/spladder/sample_alt_5prime_C3.confirmed.txt.gz
inst/extdata/example/spladder/sample_exon_skip_C3.confirmed.txt.gz
inst/extdata/example/spladder/sample_intron_retention_C3.confirmed.txt.gz
inst/extdata/example/spliceAI.vcf
inst/extdata/example/test_canonical.bed
inst/extdata/leafcutter_example.feather
inst/extdata/mmsplice_pred.csv
inst/extdata/spladder_example.feather
inst/extdata/spliceai_output.pangolin.vcf
inst/extdata/spliceai_output.vcf
inst/extdata/test_Aligned.out.sorted.bam.junc
inst/extdata/test_alt_3prime_C3.confirmed.txt.gz
inst/extdata/test_alt_5prime_C3.confirmed.txt.gz
inst/extdata/test_exon_skip_C3.confirmed.txt.gz
inst/extdata/test_intron_retention_C3.confirmed.txt.gz
inst/extdata/test_mutex_exons_C3.confirmed.txt.gz
inst/extdata/test_perind.counts.gz
man/add_context_seq.Rd
man/add_identified_in_RNA.Rd
man/add_peptide.Rd
man/add_tx.Rd
man/annotate_exon_idx.Rd
man/annotate_junc_in_orf.Rd
man/annotate_mmsplice.Rd
man/annotate_mut_effect.Rd
man/annotate_truncated_cds.Rd
man/bed_to_junc.Rd
man/breakpoint2junc.Rd
man/canonical_juncs.Rd
man/canonical_junctions.Rd
man/choose_tx.Rd
man/classify_junc_tx.Rd
man/combine_mut_junc.Rd
man/effect_to_junction_rules.Rd
man/exon_in_intron.Rd
man/figures/README-unnamed-chunk-2-1.png
man/figures/README-unnamed-chunk-3-1.png
man/format_pangolin.Rd
man/format_spliceai.Rd
man/generate_combined_dataset.Rd
man/generate_junction_id.Rd
man/get_exon_inclusion_junction.Rd
man/get_exon_skipping_junction.Rd
man/get_intronretention_alt_pos.Rd
man/get_intronretention_genomic_alt_pos.Rd
man/get_junc_pos.Rd
man/get_normalized_protein_junc_pos.Rd
man/get_peptide_context.Rd
man/get_unknown_exon_intron_retention.Rd
man/import_leafcutter_counts.Rd
man/import_spladder.Rd
man/is_canonical.Rd
man/is_first_reading_frame.Rd
man/is_in_rnaseq.Rd
man/is_start_on_exon.Rd
man/junc2breakpoint.Rd
man/junc_to_gr.Rd
man/leafcutter_transform.Rd
man/map_requant.Rd
man/modify_tx.Rd
man/next_junctions.Rd
man/pangolin_effect_translation.Rd
man/parse_gtf.Rd
man/parse_mmsplice.Rd
man/parse_pangolin.Rd
man/parse_spliceai.Rd
man/pipe.Rd
man/read_requant.Rd
man/seq_truncate_nonstop.Rd
man/sort_columns.Rd
man/spladder_transform.Rd
man/spladder_transform_ass.Rd
man/spladder_transform_exon_skipping.Rd
man/spladder_transform_format.Rd
man/spladder_transform_intron_retention.Rd
man/spladder_transform_mutex_exon.Rd
man/toy_cds.Rd
man/toy_junc_df.Rd
man/toy_junc_id.Rd
man/toy_junc_id_enst.Rd
man/toy_transcripts.Rd
man/toy_transcripts_gr.Rd
man/transform_for_requant.Rd
man/transform_leafcutter_counts.Rd
man/unique_junc_mmsplice.Rd
man/unique_mut_junc.Rd
man/unsorted_junc_df.Rd
splice2neo.Rproj
tests/spelling.R
tests/testthat.R
tests/testthat/test-add_context_seq.R
tests/testthat/test-add_peptide.R
tests/testthat/test-add_tx.R
tests/testthat/test-annotate_mut_effect.R
tests/testthat/test-bed_to_junc.R
tests/testthat/test-canonical_junctions.R
tests/testthat/test-choose_tx.R
tests/testthat/test-combine_mut_junc.R
tests/testthat/test-define_junc_id.R
tests/testthat/test-easyquant.R
tests/testthat/test-exon_in_intron.R
tests/testthat/test-format_pangolin.R
tests/testthat/test-format_spliceai.R
tests/testthat/test-get_junc_pos.R
tests/testthat/test-is_canonical.R
tests/testthat/test-junc_to_gr.R
tests/testthat/test-leafcutter_parsing.R
tests/testthat/test-mmsplice.R
tests/testthat/test-modify_tx.R
tests/testthat/test-parse_gtf.R
tests/testthat/test-parse_pangolin.R
tests/testthat/test-parse_spliceai.R
tests/testthat/test-spladder_parsing.R
tests/testthat/test-standardize_junctions_RNA_tools.R
tests/testthat/test-unique_mut_junc.R
tests/testthat/test-visualisation_junctions.R
vignettes/splice2neo_vignette.bib
vignettes/splice2neo_workflow.Rmd
