Files in JakobPedersenLab/dreams
Deep Read-level Error Model for Sequencing data
.Rbuildignore
.Rprofile
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
R/call_cancer-em_utils.R
R/call_cancer-em_utils_indels.R
R/call_cancer-statistics.R
R/call_cancer.R
R/call_cancer_indels.R
R/call_mutations-em_utils.R
R/call_mutations.R
R/call_mutations_indels.R
R/extract_features_from_bam.R
R/extract_features_from_bam_indels.R
R/get_read_positions_from_BAM.R
R/get_read_positions_from_BAM_indels.R
R/get_training_data.R
R/get_training_data_indels.R
R/load_BAM.R
R/predict_error_rates.R
R/predict_error_rates_indels.R
R/read_mutations_df_indels.R
R/sequence_position_handling.R
R/sequence_position_handling_indels.R
R/train_model.R
R/train_model_indels.R
README.Rmd
README.md
dreams.Rproj
inst/extdata/bed_cov0.bed
inst/extdata/bed_cov1.bed
inst/extdata/bed_cov2.bed
inst/extdata/bed_cov3.bed
inst/extdata/empty_example.bam
inst/extdata/empty_example.sam
inst/extdata/mini_example.bam
inst/extdata/mini_example.bam.bai
inst/extdata/mini_example.sam
inst/extdata/mini_example_no_umi.bam
inst/extdata/mini_example_no_umi.bam.bai
inst/extdata/mini_example_no_umi.sam
inst/extdata/model_test.h5
inst/extdata/positions_to_exclude_1.csv
inst/extdata/positions_to_exclude_2.csv
inst/extdata/read_example.bam
inst/extdata/read_example.bam.bai
inst/extdata/read_example.sam
inst/extdata/ref.fasta
inst/extdata/ref.fasta.fai
inst/extdata/training_data.csv
man/bed_to_granges.Rd
man/calc_string_entropy_k_mer.Rd
man/call_cancer.Rd
man/call_cancer_indels.Rd
man/call_mutations.Rd
man/call_mutations_indels.Rd
man/clean_insertions.Rd
man/convert_to_cigar.Rd
man/correct_pos_idx_w_cigar.Rd
man/correct_seq.Rd
man/dreams_cc.Rd
man/dreams_cc_indels.Rd
man/dreams_vc.Rd
man/dreams_vc_indels.Rd
man/dreams_vc_parallel.Rd
man/expand_cigar.Rd
man/extract_features_from_bam.Rd
man/extract_features_from_bam_indels.Rd
man/extract_indel_info.Rd
man/extract_mismatch_positions.Rd
man/filter_mismatch_positions.Rd
man/fit_model.Rd
man/fit_model_indels.Rd
man/generate_NN_structure.Rd
man/generate_NN_structure_indels.Rd
man/get_indel_genomic_pos.Rd
man/get_indel_info.Rd
man/get_indel_length.Rd
man/get_indel_type.Rd
man/get_indels_start_positions.Rd
man/get_match_genomic_pos_list.Rd
man/get_mismatch_genomic_pos_list.Rd
man/get_read_positions_from_BAM.Rd
man/get_read_positions_from_BAM_indels.Rd
man/get_reference_seq.Rd
man/get_training_data.Rd
man/get_training_data_from_bam.Rd
man/get_training_data_from_bam_indel.Rd
man/get_training_data_indels.Rd
man/hardclip_correct_umi_features.Rd
man/load_BAM.Rd
man/prepare_input_layer.Rd
man/prepare_input_layer_indels.Rd
man/prepare_training_data.Rd
man/prepare_training_data_indels.Rd
man/read_mutations_df.Rd
man/remove_hardclips.Rd
man/remove_softclips.Rd
man/sample_negative_read_positions.Rd
man/sample_negative_read_positions_indels.Rd
man/strand_correct_umi_features.Rd
man/train_dreams_model.Rd
man/train_dreams_model_indels.Rd
tests/testthat/inst/extdata/model_test.h5
tests/testthat/test-call_cancer.R
tests/testthat/test-call_mutations.R
tests/testthat/test-correct_pos_idx_w_cigar.R
tests/testthat/test-expand_cigar.R
tests/testthat/test-extract_features_from_BAM_indels.R
tests/testthat/test-extract_features_from_bam.R
tests/testthat/test-get_read_positions_from_BAM.R
tests/testthat/test-get_training_data.R
tests/testthat/test-load_BAM.R
tests/testthat/test-remove_softclips.R
tests/testthat/test-sequence_position_handling.R
tests/testthat/test-sequence_position_handling_indels.R
tests/testthat/test-train_model.R
