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Knetminer 3.0 #337

Merged
merged 57 commits into from Feb 22, 2019
Merged

Knetminer 3.0 #337

merged 57 commits into from Feb 22, 2019

Commits on Feb 16, 2019

  1. Merge pull request #318 from AjitPS/knetminer-3.0 

    Update Dockerfile-local
    @AjitPS
    AjitPS committed Feb 16, 2019
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  2. update gene rank to use median evidence weights 

    Take the mean of evidence weights (igf, lucene, distance), instead of multiplying them, this should lead to higher total score values.
    @KeywanHP
    KeywanHP committed Feb 16, 2019
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  3. fix chromosome name

    @KeywanHP
    KeywanHP committed Feb 16, 2019
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Commits on Feb 17, 2019

  1. normFactor change to number of hits 

    Instead of normalizing by size of entire gene knowledge graph (gkg), this only into account the number of all hits (subset of gkg). This basically is taking the mean of all evidence_weights. Additionally we introduce a small penalty if <3 hits are available per gene.
    @KeywanHP
    KeywanHP committed Feb 17, 2019
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Commits on Feb 18, 2019

  1. remove gene rank normalization

    @KeywanHP
    KeywanHP committed Feb 18, 2019
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  2. remove gene rank normalization

    @KeywanHP
    KeywanHP committed Feb 18, 2019
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  3. added docs

    @KeywanHP
    KeywanHP committed Feb 18, 2019
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  4. Merge pull request #320 from KeywanHP/knetminer-3.0 

    gene rank improvements
    @KeywanHP
    KeywanHP committed Feb 18, 2019
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  5. Merge pull request #292 from KeywanHP/knetminer-3.0 

    Knetminer 3.0
    @AjitPS
    AjitPS committed Feb 18, 2019
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  6. Merge pull request #293 from AjitPS/knetminer-3.0 

    Knetminer 3.0
    @AjitPS
    AjitPS committed Feb 18, 2019
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  7. Merge pull request #321 from AjitPS/master 

    from v3.0
    @AjitPS
    AjitPS committed Feb 18, 2019
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  8. Merge pull request #322 from Rothamsted/knetminer-3.0 

    Merge pull request #320 from KeywanHP/knetminer-3.0
    @AjitPS
    AjitPS committed Feb 18, 2019
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  9. Merge pull request #323 from AjitPS/knetminer-3.0 

    Merge pull request #292 from KeywanHP/knetminer-3.0
    @AjitPS
    AjitPS committed Feb 18, 2019
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  10. Merge pull request #295 from Rothamsted/knetminer-3.0 

    Knetminer 3.0
    @AjitPS
    AjitPS committed Feb 18, 2019
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  11. Update README

    @KeywanHP
    KeywanHP committed Feb 18, 2019
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Commits on Feb 20, 2019

  1. Collect publications to filter later

    pakk authored and pakk committed Feb 20, 2019
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  2. Filter publications in subGraph

    pakk authored and pakk committed Feb 20, 2019
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  3. Fix ConcurrentModificationException

    pakk authored and pakk committed Feb 20, 2019
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  4. New pubutils class

    pakk authored and pakk committed Feb 20, 2019
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  5. Convert in-line conceptYear to method call

    pakk authored and pakk committed Feb 20, 2019
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Commits on Feb 21, 2019

  1. filter network in no-keyword and no-keyword-match modes

    pakk authored and pakk committed Feb 21, 2019
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  2. Fix missing gene and relations

    pakk authored and pakk committed Feb 21, 2019
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  3. Fix nullpointer

    pakk authored and pakk committed Feb 21, 2019
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  4. fix missing relations and tidy up highlightPath method

    pakk authored and pakk committed Feb 21, 2019
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  5. Export only most recent papers for Gene View table

    pakk authored and pakk committed Feb 21, 2019
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Commits on Feb 22, 2019

  1. Fix network for no-keyword-match mode

    pakk authored and pakk committed Feb 22, 2019
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  2. Fix to evidence string

    pakk authored and pakk committed Feb 22, 2019
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  3. Merge pull request #296 from Rothamsted/201902_pubfilter 

    201902 pubfilter
    @AjitPS
    AjitPS committed Feb 22, 2019
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  4. evidence_nodes filtering

    @AjitPS
    AjitPS committed Feb 22, 2019
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  5. Merge pull request #324 from AjitPS/ara_pub_filter 

    Ara pub filter
    @AjitPS
    AjitPS committed Feb 22, 2019
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  6. add length to evidence string

    pakk authored and pakk committed Feb 22, 2019
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  7. Merge pull request #297 from Rothamsted/201902_pubfilter 

    201902 pubfilter
    @AjitPS
    AjitPS committed Feb 22, 2019
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  8. add line-brak to rows in geneTable

    @AjitPS
    AjitPS committed Feb 22, 2019
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  9. Merge pull request #325 from AjitPS/ara_pub_filter 

    Ara pub filter
    @AjitPS
    AjitPS committed Feb 22, 2019
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  10. legend_bug

    @AjitPS
    AjitPS committed Feb 22, 2019
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  11. Merge pull request #326 from AjitPS/ara_pub_filter 

    legend_bug
    @AjitPS
    AjitPS committed Feb 22, 2019
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  12. header fix - geneView

    @AjitPS
    AjitPS committed Feb 22, 2019
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  13. Merge pull request #327 from AjitPS/ara_pub_filter 

    header fix - geneView
    @AjitPS
    AjitPS committed Feb 22, 2019
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  14. evidenceBox fix in geneView col5

    @AjitPS
    AjitPS committed Feb 22, 2019
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  15. Merge pull request #328 from AjitPS/ara_pub_filter 

    evidenceBox fix in geneView col5
    @AjitPS
    AjitPS committed Feb 22, 2019
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  16. typo fix

    @AjitPS
    AjitPS committed Feb 22, 2019
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  17. Merge pull request #329 from AjitPS/ara_pub_filter 

    typo fix
    @AjitPS
    AjitPS committed Feb 22, 2019
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  18. fix logic of path highlighting

    pakk authored and pakk committed Feb 22, 2019
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  19. Merge pull request #298 from Rothamsted/201902_pubfilter 

    fix logic of path highlighting
    @AjitPS
    AjitPS committed Feb 22, 2019
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  20. fix evidences box in geneView table

    @AjitPS
    AjitPS committed Feb 22, 2019
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  21. Merge pull request #330 from AjitPS/ara_pub_filter 

     fix evidences box in geneView
    @AjitPS
    AjitPS committed Feb 22, 2019
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  22. fix

    @AjitPS
    AjitPS committed Feb 22, 2019
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  23. Merge pull request #331 from AjitPS/ara_pub_filter 

    fix
    @AjitPS
    AjitPS committed Feb 22, 2019
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  24. catch empty keyword in findQTL()

    pakk authored and pakk committed Feb 22, 2019
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  25. Merge pull request #332 from Rothamsted/201902_pubfilter 

    201902 pubfilter
    @AjitPS
    AjitPS committed Feb 22, 2019
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  26. add another keyword is empty check

    pakk authored and pakk committed Feb 22, 2019
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  27. exclude enzyme from evidence view

    pakk authored and pakk committed Feb 22, 2019
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  28. add doc

    pakk authored and pakk committed Feb 22, 2019
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  29. Merge pull request #333 from Rothamsted/201902_pubfilter 

    201902 pubfilter
    @KeywanHP
    KeywanHP committed Feb 22, 2019
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  30. fix genes are not flagged

    pakk authored and pakk committed Feb 22, 2019
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  31. Merge pull request #335 from Rothamsted/201902_pubfilter 

    fix genes are not flagged
    @KeywanHP
    KeywanHP committed Feb 22, 2019
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  32. edit wording

    @AjitPS
    AjitPS committed Feb 22, 2019
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