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DennisHeckDennisHeck
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fixed typos
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‎docs/PatchNotes.rst‎

Lines changed: 2 additions & 2 deletions
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- Introduced the -u / --genes flag. The output will be limited to the gene IDs/symbols in that file.
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- Introduced the -z / --reshape flag, which will write the gene-TF matrices in binary format.
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- Updated the TF motif collection (2.2)
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- The conversion of PSCMs to PSEMs will now be automatically done with the average GC-content of the --bed_file as background.
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- Updated the TF motif collection (2.2).
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- The conversion of PSCMs to PSEMs will now be done automatically with the average GC-content of the --bed_file as background.
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- One additional peak feature was added to the gene-TF marix, now we report NumPeaks, AvgPeakSize and AvgPeakDistance.
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- The processing order for writing the gene-TF matrices was changed. This will cause a slower calculation for one or very few activity columns, but a faster runtime for more.
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- Fixed an issue that the contact frequency pseudocount was only calculated within the range covered by gene windows. The difference in the resulting pseudocount are negligible.

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