weallen/Pyseqwill
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Python code for analysis of ChIP-seq and RNA-seq data. * DATA SOURCES FOR HMM - OMP meDIP (eventually) - Ngn meDIP (eventually) - OMP hmeDIP - Ngn hmeDIP - ICAM hmeDIP - OMP mk4 - Ngn mk4 - OMP mRNA-seq - Ngn mRNA-seq * DATA SOURCES FOR CORRELATION - transcript (knownGene) - gene (kgXref) - PhastCons 30way align (phastCons30Way) - GC content (gc5Base) - CpG island (cpgIslandExt) - repeat (simpleRepeat) * DATA MODEL Each row is a 100 bp window of the genome. WindowRow: - chr (int) - start (int) - end (int) - omp_expressed (binary) - ngn_expressed (binary) - omp_hmedip (int) - ngn_hmedip (int) - icam_hmedip (int) - omp_mk4 (int) - ngn_mk4 (int) - tss_dist (int) [-2kb..2kb] or INF - tse_dist (int) [-2kb..2kb] or INF - exon_start (binary) - coding_seq (binary) - in_gene (binary) - in_exon (binary)
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