├── ExCID_v2.0.zip ├── ExCID_v2.1 ├── Config.txt ├── ExCID.BatchScript_v2.1-threading_Final.pl ├── ExCID.grep_gene_list_pct_Final-miRNA.pl ├── ExCID.grep_gene_list_pct_Final.pl ├── ExCID_v2.1-Batch.pl ├── Get_HGNC.pl ├── bed_file-annotator_V2_CCDS-miRBASE.pl ├── bed_file-annotator_V2_RefSeq-VEGA.pl ├── bin │ ├── CapStatsV2.5.jar │ ├── CapStatsV2.6.jar │ ├── CovFasta_Generator.jar │ ├── Java_code │ │ ├── CaptureStatsBAM5_extended.java │ │ ├── ParseOpts.java │ │ ├── WGS_Stats_v1.java │ │ ├── picard-1.88.jar │ │ └── sam-1.88.jar │ ├── WGSStats_v1.1.jar │ └── WGSStats_v1.jar ├── change_log.txt ├── check_HGNC_individual_CCDSDB.pl ├── check_HGNC_individual_RefSeqDB.pl ├── check_HGNC_individual_VEGADB.pl ├── check_HGNC_individual_mirnaDB.pl ├── creat_bed_UCSC_coding.pl ├── database.tgz ├── external_programs │ └── BEDTools.v2.17.0.tar.gz ├── miRBASE_r20.gff2 ├── reformat.pl ├── setup.sh └── update_databases.sh └── README.md /ExCID_v2.0.zip: 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