yocra3 epimutacions issues

yocra3 / epimutacions

Package to detect epimutations from DNA methylation data

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Task1 feature beta diff

#82 jamesbaye opened 3 years ago
0
Task1 refactor epimutations: separate dataframe creation and filtering

#81 jamesbaye opened 3 years ago
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updated epimutations docstring

#80 jamesbaye closed 3 years ago
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Update EpIsolationForest and some documentation

#79 LeireAbarrategui opened 3 years ago
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Added plotting function but it is not functional yet. Needs testing

#78 RaqManzano opened 3 years ago
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Task1 refactor manova mlm

#77 jamesbaye closed 3 years ago
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Task1 test all methods return toy epimutation

#76 jamesbaye closed 3 years ago
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Update, filtering needs rellocation

#75 carleshf closed 3 years ago
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toy datasets contain more samples

#74 pavlohrab closed 3 years ago
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Task1 bugfix integrate manova mlm

#73 jamesbaye closed 3 years ago
1
Task 11 12

#72 LeireAbarrategui closed 3 years ago
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Task1 feature report multiple outlier scores

#71 jamesbaye closed 3 years ago
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Revert "Added statistics in epiManova and epiMLM"

#70 LeireAbarrategui closed 3 years ago
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Added statistics in epiManova and epiMLM

#69 LeireAbarrategui closed 3 years ago
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Task2b

#68 carleshf closed 3 years ago
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Task3

#67 yocra3 closed 3 years ago
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Substituting data.table function to core R

#66 RaqManzano closed 3 years ago
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Added documentation + examples. Also improved speed.

#65 carleshf closed 3 years ago
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Task 17. Draft a vignette for the package

#64 carleshf opened 3 years ago
1
epimutations() edge case tests and minor fixes

#63 jamesbaye closed 3 years ago
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Task3b - Added OMIM annotation and added comments to function

#62 RaqManzano closed 3 years ago
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num.cpgs now defaults to 3

#61 jamesbaye closed 3 years ago
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all 20 CpG are now within 1000 bp sequence

#60 pavlohrab closed 3 years ago
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Updated toy datasets

#59 pavlohrab closed 3 years ago
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hotfix corrected - formula generalises to length(sample_ids)>=1

#58 jamesbaye closed 3 years ago
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fix incorrect raise if sample_ids is missing

#57 jamesbaye closed 3 years ago
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Task3a illumina annotation

#56 RaqManzano closed 3 years ago
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Changed epi_manova and added in epimutations

#55 LeireAbarrategui closed 3 years ago
1
Task1 feature make control optional

#54 jamesbaye closed 3 years ago
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Task3a - illumina annotation to output: gene, feature and relation to…

#53 RaqManzano closed 3 years ago
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Task3d

#52 yocra3 closed 3 years ago
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Task1 merge bugfix and docstring update

#51 jamesbaye closed 3 years ago
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Changed manova function

#50 LeireAbarrategui closed 3 years ago
1
added man/ to .gitignore

#49 jamesbaye closed 3 years ago
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Task2b

#48 carleshf closed 3 years ago
2
Task15

#47 pavlohrab closed 3 years ago
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epimutations() sample_ids argument now runs on a set of samples

#46 jamesbaye closed 3 years ago
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improve EpiMutations() output

#45 jamesbaye closed 3 years ago
6
commit man files

#44 jamesbaye closed 3 years ago
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Task1ab feature cases as controls

#43 jamesbaye closed 3 years ago
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Added genomicratioset dataset, created from methylation_matrix

#42 pavlohrab closed 3 years ago
1
Task15

#41 pavlohrab closed 3 years ago
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refactored epimutations() into subfunctions

#40 jamesbaye closed 3 years ago
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Task 3d. Add ENSEMBL regulatory elements

#39 yocra3 closed 3 years ago
1
Task 3c. Add gnomAD data

#38 yocra3 opened 3 years ago
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Task 3b. Add OMIM data

#37 yocra3 opened 3 years ago
2
Task 3a. Add illumina annotation

#36 yocra3 opened 3 years ago
2
fixed some errors due to variable name typos and incorrect ranges

#35 jamesbaye closed 3 years ago
0
Task1

#34 carleshf closed 3 years ago
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dependency is R >= 3.6

#33 jamesbaye closed 3 years ago
1