Files in theron-palmer/splicemute
splicemute
.Rbuildignore
.Rproj.user/9F234233/sources/prop/0CD4AEBF
.Rproj.user/9F234233/sources/prop/1D8251E0
.Rproj.user/9F234233/sources/prop/621D0AED
.Rproj.user/9F234233/sources/prop/A0AA321F
.Rproj.user/9F234233/sources/prop/ACF8A599
.Rproj.user/9F234233/sources/prop/C6062C45
.Rproj.user/9F234233/sources/prop/C9AB0E89
.Rproj.user/9F234233/sources/prop/INDEX
.Rproj.user/shared/notebooks/patch-chunk-names
.Rproj.user/shared/notebooks/paths
.gitattributes
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/.ipynb_checkpoints/functions-checkpoint.R
R/functions.R
README.md
inst/.ipynb_checkpoints/TCGA_assign_imm-checkpoint.py
inst/.ipynb_checkpoints/TCGA_persamp_summary-checkpoint.py
inst/.ipynb_checkpoints/TCGA_persamp_tumor_kmers-checkpoint.py
inst/.ipynb_checkpoints/Untitled-checkpoint.ipynb
inst/.ipynb_checkpoints/calc_perc_rank-checkpoint.py
inst/.ipynb_checkpoints/comb_files-checkpoint.py
inst/.ipynb_checkpoints/extract_data-checkpoint.py
inst/.ipynb_checkpoints/extract_percentile-checkpoint.py
inst/.ipynb_checkpoints/pep_similarity-checkpoint.py
inst/.ipynb_checkpoints/process_bindaff-checkpoint.py
inst/.ipynb_checkpoints/process_peptides-checkpoint.py
inst/.ipynb_checkpoints/process_percentile-checkpoint.py
inst/.ipynb_checkpoints/reduce_percentile-checkpoint.py
inst/.ipynb_checkpoints/runMHCnuggets-checkpoint.py
inst/.ipynb_checkpoints/runMHCnuggets_ind-checkpoint.py
inst/.ipynb_checkpoints/splicemutr-checkpoint.py
inst/.ipynb_checkpoints/txt_to_fa-checkpoint.py
inst/TCGA_assign_imm.py
inst/TCGA_persamp_summary.py
inst/TCGA_persamp_tumor_kmers.py
inst/Untitled.ipynb
inst/__pycache__/splicemutr.cpython-39.pyc
inst/calc_perc_rank.py
inst/comb_files.py
inst/extract_data.py
inst/extract_percentile.py
inst/pep_similarity.py
inst/process_bindaff.py
inst/process_peptides.py
inst/process_percentile.py
inst/reduce_percentile.py
inst/runMHCnuggets.py
inst/runMHCnuggets_ind.py
inst/splicemutr.py
inst/txt_to_fa.py
man/adjust_width.Rd
man/check_tx.Rd
man/choose_exons.Rd
man/choose_transcripts.Rd
man/countKmers.Rd
man/create_cds.Rd
man/extract_transcripts.Rd
man/find_genes.Rd
man/find_introns.Rd
man/find_orfs.Rd
man/format_introns.Rd
man/getUniqKmers.Rd
man/is_UTR.Rd
man/junc_loc_pep.Rd
man/mod_made.Rd
man/modify_cds.Rd
man/running_sum.Rd
man/split_kmers.Rd
man/star_to_leaf.Rd
man/which_codon.Rd
man/which_junctions_overlap.Rd
manuscript/bioinformatics.csl
manuscript/library.bib
manuscript/manuscript.Rmd
manuscript/manuscript.docx
manuscript/manuscript.html
scripts/STAR_to_leaf.R
scripts/TCGA_assign_imm.R
scripts/TCGA_combine_kmers.R
scripts/TCGA_gene_expr_per_sample.R
scripts/TCGA_mut_sig.R
scripts/TCGA_persamp_metrics.R
scripts/TCGA_persamp_metrics_ann.R
scripts/TCGA_persamp_metrics_ann_jun_summ.R
scripts/TCGA_persamp_metrics_jun_summ.R
scripts/TCGA_persamp_tum_kmers.R
scripts/calc_gene_metric.R
scripts/calc_gene_metric_TCGA.R
scripts/combine_data_splicemutr.sh
scripts/combine_featurecounts.R
scripts/create_TMB_TCGA_maf_summary.R
scripts/create_hotspots.R
scripts/create_junc_expr.R
scripts/create_junc_expr_TCGA.R
scripts/create_kmer_file.R
scripts/extract_peptides.R
scripts/filter_juncs.R
scripts/form_transcripts.R
scripts/form_transcripts_ali.R
scripts/form_transcripts_tcga.R
scripts/make_txdb.R
scripts/process_arcashla.R
scripts/rds_to_txt.R
scripts/recount3_tcga_juncs.R
scripts/run_fgsea.R
scripts/save_introns.R
scripts/split_introns.R
scripts/valsamo_analyze_splicemutr.R
scripts/valsamo_create_comparisons.R
splicemute.Rproj
