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Proliferation model (initial version) and improved mapping #44

Merged
merged 33 commits into from
Nov 1, 2024
Merged

Proliferation model (initial version) and improved mapping #44

merged 33 commits into from
Nov 1, 2024

Commits on Jul 2, 2024

  1. clearer error message in QC

    @jykr
    jykr committed Jul 2, 2024
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Commits on Aug 14, 2024

  1. adding per-replicate LFC and total editing rate

    @jykr
    jykr committed Aug 14, 2024
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  2. output editing rate also for uniform mode

    @jykr
    jykr committed Aug 14, 2024
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  3. remove reordering of columns to troubleshoot dataset without editing … 

    …rate
    @jykr
    jykr committed Aug 14, 2024
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Commits on Aug 15, 2024

  1. adjustments for survival models

    @jykr
    jykr committed Aug 15, 2024
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Commits on Aug 16, 2024

  1. debug non-numeric error for time column

    @jykr
    jykr committed Aug 16, 2024
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Commits on Aug 23, 2024

  1. allow user-provided control-conditions

    @jykr
    jykr committed Aug 23, 2024
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Commits on Aug 26, 2024

  1. debug errors in calculating edits

    @jykr
    jykr committed Aug 26, 2024
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  2. allow 0 edit counts

    @jykr
    jykr committed Aug 26, 2024
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  3. debug sample ordering

    @jykr
    jykr committed Aug 26, 2024
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Commits on Aug 27, 2024

  1. twoctrls6

    @jykr
    jykr committed Aug 27, 2024
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  2. twoctrls7

    @jykr
    jykr committed Aug 27, 2024
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  3. twoctrls8

    @jykr
    jykr committed Aug 27, 2024
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  4. twoctrls9

    @jykr
    jykr committed Aug 27, 2024
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  5. twoctrls10

    @jykr
    jykr committed Aug 27, 2024
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Commits on Aug 28, 2024

  1. twoctrls11

    @jykr
    jykr committed Aug 28, 2024
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Commits on Aug 29, 2024

  1. set correct mu0 for nonedited

    @jykr
    jykr committed Aug 29, 2024
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  2. don't allow training of mu0 with non-negctrl

    @jykr
    jykr committed Aug 29, 2024
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  3. model16

    @jykr
    jykr committed Aug 29, 2024
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  4. model18

    @jykr
    jykr committed Aug 29, 2024
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  5. model20

    @jykr
    jykr committed Aug 29, 2024
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  6. model21

    @jykr
    jykr committed Aug 29, 2024
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Commits on Sep 4, 2024

  1. model24

    @jykr
    jykr committed Sep 4, 2024
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  2. model25: normalize by total abundance

    @jykr
    jykr committed Sep 4, 2024
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  3. model26

    @jykr
    jykr committed Sep 4, 2024
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Commits on Sep 5, 2024

  1. model29

    @jykr
    jykr committed Sep 5, 2024
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  2. model30: should I double the norm factor?

    @jykr
    jykr committed Sep 5, 2024
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  3. model31

    @jykr
    jykr committed Sep 5, 2024
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Commits on Sep 6, 2024

  1. model31

    @jykr
    jykr committed Sep 6, 2024
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Commits on Oct 2, 2024

  1. tiling screen update

    @jykr
    jykr committed Oct 2, 2024
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Commits on Oct 15, 2024

  1. filter out R2 with too short reporter length

    @jykr
    jykr committed Oct 15, 2024
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Commits on Nov 1, 2024

  1. allow duplicated matching to the best match

    @jykr
    jykr committed Nov 1, 2024
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  2. pin docutils version for Sphinx

    @jykr
    jykr committed Nov 1, 2024
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