TRON-Bioinformatics/splice2neo
Aberrant splice junction analysis with associated mutations

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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
Docker/Dockerfile
Docker/README.md
Docker/build_docker.sh
Docker/splice2neo.def
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_cispliceai.R R/format_pangolin.R R/format_spliceai.R R/get_junc_pos.R R/globals.R R/irfinder_parsing.R R/is_canonical.R R/is_in_rnaseq.R R/junc_to_gr.R R/leafcutter_parsing.R R/liftover_junc_id.R R/mmsplice.R R/modify_tx.R R/parse_cispliceai.R R/parse_gtf.R R/parse_pangolin.R R/parse_regtools.R R/parse_spliceai.R R/parse_star.R R/parse_stringtie.R R/parse_suppa2.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/GFF3_files/a.gff3
inst/extdata/GTF_files/Aedes_aegypti.partial.gtf
inst/extdata/IRFinder-IR-nondir-val.txt
inst/extdata/IRFinder-IR-nondir.txt
inst/extdata/cispliceai_thresh_output.empty.vcf
inst/extdata/cispliceai_thresh_output.vcf
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/spliceai_thresh_output.vcf
inst/extdata/test.chain
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
inst/extdata/test_regtools_Aligned.out.sorted.bam.junc
inst/extdata/test_star_SJ.out.tab
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/effect_to_junction_rules_wo_ir.Rd man/exon_in_intron.Rd
man/figures/README-unnamed-chunk-2-1.png
man/figures/README-unnamed-chunk-3-1.png
man/filter_irfinder_txt.Rd man/format_cispliceai_thresh.Rd man/format_pangolin.Rd man/format_spliceai.Rd man/format_spliceai_thresh.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_irfinder_txt.Rd man/import_leafcutter_counts.Rd man/import_regtools_junc.Rd man/import_spladder.Rd man/import_star_sj.Rd man/import_stringtie_gtf.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/liftover_junc_id.Rd man/map_requant.Rd man/modify_tx.Rd man/next_junctions.Rd man/pangolin_effect_translation.Rd man/parse_cispliceai_thresh.Rd man/parse_gtf.Rd man/parse_irfinder_txt.Rd man/parse_mmsplice.Rd man/parse_pangolin.Rd man/parse_spliceai.Rd man/parse_spliceai_thresh.Rd man/parse_star_sj.Rd man/pipe.Rd man/read_requant.Rd man/read_suppa_ioe.Rd man/regtools_transform.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/stringtie_transform.Rd man/stringtie_transform_format.Rd man/suppa_import.Rd man/suppa_transform.Rd man/suppa_transform_format.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_irfinder_txt.Rd man/transform_leafcutter_counts.Rd man/transform_regtools_junc.Rd man/transform_star_sj.Rd man/transform_suppa_ass_events.Rd man/transform_suppa_ir_events.Rd man/transform_suppa_mxe_events.Rd man/transform_suppa_se_events.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_cispliceai.R tests/testthat/test-format_pangolin.R tests/testthat/test-format_spliceai.R tests/testthat/test-get_junc_pos.R tests/testthat/test-irfinder_parsing.R tests/testthat/test-is_canonical.R tests/testthat/test-junc_to_gr.R tests/testthat/test-leafcutter_parsing.R tests/testthat/test-liftover_junc_id.R tests/testthat/test-mmsplice.R tests/testthat/test-modify_tx.R tests/testthat/test-parse_cispliceai.R tests/testthat/test-parse_gtf.R tests/testthat/test-parse_pangolin.R tests/testthat/test-parse_regtools.R tests/testthat/test-parse_spliceai.R tests/testthat/test-parse_star.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
TRON-Bioinformatics/splice2neo documentation built on Nov. 9, 2024, 5:28 p.m.

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