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major code changes and logical improvements in analysis steps #61

Merged
merged 27 commits into from
May 19, 2024
Merged

major code changes and logical improvements in analysis steps #61

merged 27 commits into from
May 19, 2024

Commits on May 15, 2024

  1. improve input args

    @abearab
    abearab committed May 15, 2024
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  2. increase max value for num_pseudogenes

    @abearab
    abearab committed May 15, 2024
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  3. mend

    @abearab
    abearab committed May 15, 2024
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  4. mend

    @abearab
    abearab committed May 15, 2024
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  5. mend

    @abearab
    abearab committed May 15, 2024
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Commits on May 16, 2024

  1. add log2 option

    @abearab
    abearab committed May 16, 2024
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  2. improve count normalization

    @abearab
    abearab committed May 16, 2024
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  3. mend

    @abearab
    abearab committed May 16, 2024
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  4. mend

    @abearab
    abearab committed May 16, 2024
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  5. mend

    @abearab
    abearab committed May 16, 2024
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  6. mend

    @abearab
    abearab committed May 16, 2024
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  7. change how to generate pseudo genes

    @abearab
    abearab committed May 16, 2024
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  8. mend

    @abearab
    abearab committed May 16, 2024
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  9. draft Kolmorogov-Smirnov test

    @abearab
    abearab committed May 16, 2024
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  10. mend

    @abearab
    abearab committed May 16, 2024
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  11. mend

    @abearab
    abearab committed May 16, 2024
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  12. change countNormalization

    @abearab
    abearab committed May 16, 2024
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  13. fix sort order

    @abearab
    abearab committed May 16, 2024
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  14. fix sort order

    @abearab
    abearab committed May 16, 2024
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  15. change countNormalization

    @abearab
    abearab committed May 16, 2024
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  16. fix code order 

    thanks to Nick's comments!
    @abearab
    abearab committed May 16, 2024
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  17. mend

    @abearab
    abearab committed May 16, 2024
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Commits on May 17, 2024

  1. mend

    @abearab
    abearab committed May 17, 2024
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  2. mend

    @abearab
    abearab committed May 17, 2024
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  3. change test level

    @abearab
    abearab committed May 17, 2024
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Commits on May 19, 2024

  1. add a key step 

    remove duplicate sequences in library as it doesn't make sense to have it for fastq2count task
    @abearab
    abearab committed May 19, 2024
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  2. update version

    @abearab
    abearab committed May 19, 2024
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