Improved paired-end support + update to snakemake 8.10.7

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Fixed ftp connection issue

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Improved Differential Expression analysis and metagene profiling

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Fixed orientations for all differential expression tools

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Bugfix for differential expression when using newer R versions

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Improvements to differential expression analysis

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Fixed compatibility issues with newer snakemake versions +more

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Improved xlsx files and gff2 handling

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Improved gff2 handling

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Bugfix overview_excel.py

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