https://github.com/qqwang-berkeley/JUM
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Tip revision: afeaab37960ac19b78511e8909b5e630ec355751 authored by Qingqing Wang on 10 April 2023, 14:50:26 UTC
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Identify_intron_retention_event_exist_in_all_samples.pl -rw-r--r-- 1.4 KB
Identify_junctions_exist_in_all_samples.pl -rw-r--r-- 1.7 KB
Identify_junctions_exist_in_certain_number_of_input_files.pl -rw-r--r-- 1.7 KB
JUM_2-1.sh -rw-r--r-- 581 bytes
JUM_2-2.sh -rw-r--r-- 2.4 KB
JUM_A.sh -rw-r--r-- 19.7 KB
JUM_A_multi_1.sh -rw-r--r-- 14.2 KB
JUM_A_multi_2.sh -rw-r--r-- 4.4 KB
JUM_B.sh -rw-r--r-- 19.3 KB
JUM_C.sh -rw-r--r-- 10.1 KB
LICENSE -rw-r--r-- 1.0 KB
Old JUM manual for 1.3.7-1.3.11 -rw-r--r-- 23.5 KB
README.md -rw-r--r-- 1.7 KB
R_script_JUM.R -rw-r--r-- 890 bytes
count_intron_read_long_intron_retention_step1.pl -rw-r--r-- 1.5 KB
count_intron_read_long_intron_retention_step2_updated.pl -rw-r--r-- 1.1 KB
count_intron_read_long_intron_retention_step3.pl -rw-r--r-- 1.3 KB
count_reads_for_intron_retention_sam.pl -rw-r--r-- 1.4 KB
determining_rightful_long_intron_retention_event_updated.pl -rw-r--r-- 3.1 KB
determining_rightful_total_cassette_exon_event.pl -rw-r--r-- 2.0 KB
experiment_design.txt -rw-r--r-- 65 bytes
extract_intron_retention_event_coordinate_conditional_union_splicing_junction_gff.pl -rw-r--r-- 4.8 KB
extract_intron_retention_event_coordinate_from_samples_conditional_union.pl -rw-r--r-- 2.2 KB
final_process_A3SS_output.pl -rw-r--r-- 5.0 KB
final_process_A5SS_output.pl -rw-r--r-- 5.0 KB
final_process_IR_output_long.pl -rw-r--r-- 2.5 KB
final_process_IR_output_short.pl -rw-r--r-- 2.2 KB
final_process_MXE_output.pl -rw-r--r-- 10.1 KB
final_process_cassette_exon_output1.pl -rw-r--r-- 2.8 KB
final_process_cassette_exon_output1_update.pl -rw-r--r-- 2.8 KB
final_process_cassette_exon_output2.pl -rw-r--r-- 984 bytes
final_process_composite_output.pl -rw-r--r-- 3.9 KB
first_processing_generate_JUM_reference_for_profiled_total_alternative_splicing_event_junction.pl -rw-r--r-- 1.6 KB
generate_JUM_format_annotation_file_for_profiled_alternative_splicing_event_junction.pl -rw-r--r-- 3.2 KB
identify_gene_name_for_JUM_output_1.pl -rw-r--r-- 2.5 KB
identify_gene_name_for_JUM_output_2.pl -rw-r--r-- 2.1 KB
identify_gene_name_for_JUM_output_3.pl -rw-r--r-- 1.1 KB
making_junction_count_file_matching_annotation_for_JUM.pl -rw-r--r-- 1.2 KB
making_junction_count_file_matching_annotation_for_JUM_in_intron_retention.pl -rw-r--r-- 1.1 KB
output_reformat_JUM_1.pl -rw-r--r-- 1.2 KB
output_reformat_JUM_2.pl -rw-r--r-- 2.8 KB
output_reformat_JUM_3.pl -rw-r--r-- 2.8 KB
output_reformat_JUM_4.pl -rw-r--r-- 2.2 KB
prepare_count_file_after_STAR_2_pass_mapping.pl -rw-r--r-- 1.2 KB
prepare_significant_long_intron_retention_event.pl -rw-r--r-- 2.4 KB
preparing_intron_retention_count_table_long_intron.pl -rw-r--r-- 3.5 KB
preparing_intron_retention_count_table_short_intron.pl -rw-r--r-- 2.0 KB
preparing_intron_retention_event_for_JUM_combine.pl -rw-r--r-- 4.1 KB
process_raw_AS_differential_output.pl -rw-r--r-- 6.6 KB
profile_AS_events_sharing_3_prime_ss.pl -rw-r--r-- 2.0 KB
profile_AS_events_sharing_5_prime_ss.pl -rw-r--r-- 2.0 KB
profile_overhang_from_STAR_output_step_1.pl -rw-r--r-- 2.7 KB
profile_overhang_from_STAR_output_step_2.pl -rw-r--r-- 1.6 KB
profiling_splicing_patterns_from_AS_events.pl -rw-r--r-- 3.2 KB
profiling_splicing_patterns_from_AS_events_1.pl -rw-r--r-- 1.5 KB
profiling_splicing_patterns_from_AS_events_2.pl -rw-r--r-- 1.3 KB
profiling_splicing_patterns_from_AS_events_3_updated.pl -rw-r--r-- 8.7 KB
profiling_splicing_patterns_from_AS_events_4.pl -rw-r--r-- 1.6 KB
profiling_splicing_patterns_from_AS_events_5.pl -rw-r--r-- 2.4 KB
profiling_splicing_patterns_from_AS_events_6.pl -rw-r--r-- 2.4 KB
screening_A5SS_A3SS_events.pl -rw-r--r-- 1.8 KB
screening_MXE_events.pl -rw-r--r-- 5.0 KB
screening_cassette_exon_events.pl -rw-r--r-- 3.0 KB
screening_intron_retention_event_for_deltachange_consistency.pl -rw-r--r-- 2.1 KB
screening_intron_retention_event_for_no_inner_junction.pl -rw-r--r-- 1.8 KB
second_processing_generate_JUM_reference_for_profiled_total_alternative_splicing_event_junction.pl -rw-r--r-- 1.7 KB
vary_for_replicate.pl -rw-r--r-- 592 bytes

README.md

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