Files in TranslationalBioinformaticsLab/INDELfindR
Indel Detection from Human Genomic Sequence Data
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/functions.R
R/globals.R
R/indelfindr.R
README.md
demo/EGFR_mutations_indelfindr_demo.bam
demo/EGFR_mutations_indelfindr_demo.bam.bai
demo/EGFR_mutations_indelfindr_demo.validation_check.indel.cigars.csv
demo/EGFR_mutations_indelfindr_demo.validation_check.vcf
demo/EGFR_regions_of_interest.txt
demo/indelfindr_example_shell_script.sh
demo/indelfindr_example_shell_script.sh.orig
indelfindr.Rproj
man/calculate_strand_bias_pval_vaf_and_dp_parallel.Rd
man/calculate_strand_bias_pval_vaf_and_dp_parallel_each_indel.Rd
man/convert_cigar_to_verbose_string.Rd
man/filter_and_annotate_calls.Rd
man/getIndelCoverage.Rd
man/getVaf.Rd
man/get_primary_chroms.Rd
man/refine_cigar_string.Rd
man/run_algo_all_reads_each_bam_region_with_simple_indel_padding.Rd
man/run_algo_on_one_read_explicit_args_with_simple_indel_padding.Rd
man/run_indelfindr.Rd
man/seq_with_uneven_last.Rd
man/translate_cigar_index_to_ref_and_query_algo_dev_sliding.Rd
man/translate_cigar_index_to_ref_and_query_v2.Rd
man/translate_cigar_index_to_ref_and_query_v2_with_simple_indel_padding.Rd
man/translate_cigar_index_to_ref_and_query_whole_read.Rd
man/unexplode_cigar_string.Rd
man/write.vcf.Rd
vignettes/.gitignore
vignettes/indelfindr.Rmd
