Random scripts for various tasks

• CMI2NI.m

  • Conditional mutual inclusive information(CMI2)-based Network Inference method for gene expression data.
  • Author: Xiujun Zhang.

• run_CMI2NI.R

  • R wrapper for CMI2NI.m.

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• jtk_cycle_script.R
  • example script for using JTK_Cycle, an algorithm to identify rhythmic components in large, genome-scale data sets and estimate their period length, phase, and amplitude.
  • Author: Karl Kornacker and John Hogenesch.

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• doubletShuffle.py

  • Script for shuffling a sequence while preserving the doublet fequency.
  • Author: Babak Alipanahi

• oneHot.py

  • Script to transform DNA sequence into ordinal matrix (One-hot encoding)

• shortenSequences.py

  • Script to shorten file containing sequences of various length to user-defined length from both ends equally.

• generateDeepBindInput.R

  • Script to generate valid DeepBind input files from two files containing DNA sequences.

• getPeakSequences.sh

  • Get DNA sequences from reference genome matching top peaks.

• genmaster.sh

  • Master script to get peak sequences from peakfiles and generate fasta files.

• genUCSCbed.sh

  • Add to a folder of bed-files header info to be compatible with UCSC genome browser.

• pool_top_chip_peaks.sh

  • Pool multiple chip files together under one data series folder.

• bed2fasta.sh

  • Get DNA sequences from reference genome matching bed-file.

• fasta2deepbind.sh

  • Convert fasta file to DeepBind input by splitting sequences to train and test inputs and optionally shorten the sequences.

• genmaster2.sh

  • Master script to convert folder of bed-files to fasta-files.

• DinucShuffle.py

  • Shuffle fasta or plain sequence files with dinucleotide shuffle.

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• pickle2pfms.py

  • Convert DeepBind pickle-files to PFMs.

• pfms2motif.R

  • Plot PFMs as motif logos.

• pkl2motif.sh

  • Master script to convert DeepBind pickle-files to motif logos.

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