An integrated resource and analysis platform for human eccDNAs. Also see homepage
- bedtools 2.0 or higher doc
- python 3.7 www.python.org
- numpy www.numpy.org
- scipy www.scipy.org
- other common packages: multiprocessing and argparse
tips: Anaconda is always a good choice to install the dependencies.
- Chromatin_access.bed download
- Chromatin_interaction.bed download
- Epigenetic_regulation.bed download
- Genetic_variant.bed download
- Regulatory_elements.bed download
- Targeting_genes.bed download
- eccDNA_core.hg19.bed download
- Go to the scoring system directory and set all the dependencies
- Download all the input files listed above and decompress them
- Run the run.sh shell script
- hits.stat.* files are annotated hits (records) count for each eccDNA in six regulatory categories. The last field is the count number.
- *.score files inlcude score for each eccDNA corresponding Gaussian mode in six regulatory categories. Here are the fields:
- eccDNA id.
- Chromosome to which the eccDNA belongs.
- Hits number for the eccDNA.
- Hits number after Box-Cox transformation for the eccDNA.
- Mean of the hits number for all eccDNAs at chromosome list on the second field (i.e., 𝜇 of the Gaussian distribution).
- Standard Deviation of the hits number for all eccDNAs at chromosome list on the second field (i.e., 𝜎 of the Gaussian distribution).
- Probability greater than the hits number in the corresponding Gaussian distribution.
- The score for the eccDNA (i.e., negative of the base 10 logarithm of the Probability).
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*.nor files include normalized score of each category. The first 8 columns are same as *.score files, column 9 is the Z-score of the regulatory category and column 10 is the normalized score.
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final.score.txt file is the final result we want. Here are the fields:
- eccDNA id.
- Average of normalized scores for all six regulatory categories.
You can download all output here