chiptoolkit

Tools for analyzing chip-seq like data

• dumpHDF5.py

  Compute per base coverage from a 1-based bedgraph format file, then dump into the specified hdf5 file

• loadHDF5.py

  Load coverage in the regions provided, output the average coverage per base, heatmap and composite plot. All regions must have the same length

• loadHDF5_mpi.py

  MPI version of loadHDF5.py

• loadHDF5_pearson.py

  Load genome-wide coverage or coverage in the regions if provided region file, concatenate them and chop into bins, compute pearson/spearman correlation of these bins, output correlation matrix, heatmap.

• loadHDF5_pearson_mpi.py

  MPI version of loadHDF5_pearson_mpi.py