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base repository: pachterlab/sleuth
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head repository: pachterlab/sleuth
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compare: devel
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  • 20 commits
  • 27 files changed
  • 3 contributors

Commits on Jun 7, 2018

  1. fix sanity check when setting pval_aggregate to TRUE; add sanity chec… 

    …k when setting gene_mode to TRUE
    @warrenmcg
    warrenmcg committed Jun 7, 2018
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  2. additional sanity checks for aggregation_column

    @warrenmcg
    warrenmcg committed Jun 7, 2018
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  3. fix the sanity checks for changing the transform functions 

    + this also includes a sanity check for sleuth_fit to make sure it is not run when other fits are already not synced
+ this is to preserve provenance when exchanging sleuth objects
    @warrenmcg
    warrenmcg committed Jun 7, 2018
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  4. update the ellahi test datasets to v0.30.0

    @warrenmcg
    warrenmcg committed Jun 7, 2018
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  5. in helper script for testing, load the updated test datasets, and cre… 

    …ate a test dataset ready for pvalue aggregation testing
    @warrenmcg
    warrenmcg committed Jun 7, 2018
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  6. add several additional tests: 

    + test duplicate IDs
+ test changing transformation functions
+ test changing normalization functions
+ test changing gene_column, gene_mode, and pval_aggregate
+ test pval aggregation (though in this simple case, no actual aggregation occurs)
    @warrenmcg
    warrenmcg committed Jun 7, 2018
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Commits on Jun 8, 2018

  1. Merge pull request #182 from warrenmcg/patch_0.30 

    Improved sanity checks and testing
    @pimentel
    pimentel authored Jun 8, 2018
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Commits on Mar 14, 2019

  1. fix bug found in #204 where abundance matrix does not subset correctly

    @warrenmcg
    warrenmcg committed Mar 14, 2019
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  2. address #197 by coercing kallisto path to character

    @warrenmcg
    warrenmcg committed Mar 14, 2019
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Commits on Mar 15, 2019

  1. fix how default values are displayed for transcript view, gene view, … 

    …and heat map
    @warrenmcg
    warrenmcg committed Mar 15, 2019
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  2. add missing download buttons 

    + can now download LRT test table and fragment length distribution plot
+ this partially addresses #62 (only one missing is multi-transcript gene view when gene_mode is FALSE)
    @warrenmcg
    warrenmcg committed Mar 15, 2019
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  3. fix typo found in #212 and update documentation

    @warrenmcg
    warrenmcg committed Mar 15, 2019
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  4. fix dependency issue with utils::head seen in #135

    @warrenmcg
    warrenmcg committed Mar 15, 2019
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  5. provide more informative error reporting when reading kallisto HDF5 f… 

    …iles

+ This should make it clear to users when issue uncovered in #120 might apply
    @warrenmcg
    warrenmcg committed Mar 15, 2019
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Commits on Mar 16, 2019

  1. fix bug where transcripts would still cluster even if cluster_transcr… 

    …ipts = FALSE

+ this fixes error found in #208
    @warrenmcg
    warrenmcg committed Mar 16, 2019
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  2. guarantee the order of transcripts given to plot_transcript_heatmap i… 

    …f cluster_transcripts is FALSE

+ this fixes the bug identified in #207
    @warrenmcg
    warrenmcg committed Mar 16, 2019
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Commits on Dec 17, 2019

  1. Merge pull request #214 from warrenmcg/patch_misc 

    Miscellaneous bug fixes
    @pimentel
    pimentel authored Dec 17, 2019
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  2. add back in deleted 'gene_from_gene' method to fix #190

    @warrenmcg @pimentel
    warrenmcg authored and pimentel committed Dec 17, 2019
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  3. merge conflict in documentation #talon

    @pimentel
    pimentel committed Dec 17, 2019
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  4. Merge branch 'andrewrech-master' into devel

    @pimentel
    pimentel committed Dec 17, 2019
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