mpi2 impc_stats_pipeline issues

mpi2 / impc_stats_pipeline

R packages for the stats pipeline

https://www.mousephenotype.org/

Apache License 2.0

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issues

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Get rid of `ReplaceWordInFile` function

#95 marinak-ebi opened 4 days ago
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Refactor `updateImpress` to use newly generated `metadataParameters.csv` instead of updating DRrequiredAgeing package locally

#94 marinak-ebi opened 4 days ago
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Get rid of list of genes `ignoromeGenes` that is not in use anymore

#93 marinak-ebi opened 3 weeks ago
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Get rid of hardcoded GitHub link

#92 marinak-ebi opened 3 weeks ago
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Move orchestration from inside the pipeline to an external layer

#91 marinak-ebi opened 1 month ago
1
Migrate from Conda

#90 marinak-ebi opened 1 month ago
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Get rid of `EquationMap.conf` and functions that process this file

#89 marinak-ebi opened 1 month ago
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Get rid of `EquationMap.conf` and code associated with the file

#88 marinak-ebi opened 1 month ago
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Remove the statistical pipeline unused code

#87 marinak-ebi closed 1 month ago
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Update `LICENSE` copyright owner

#86 marinak-ebi closed 1 month ago
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Write script `run_pipeline.sh` that run both statistical and annotation pipeline

#85 marinak-ebi closed 1 month ago
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Write script that run both statistical and annotation pipeline

#84 marinak-ebi opened 1 month ago
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Upgrade to R version 4.4

#83 marinak-ebi opened 2 months ago
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Recreate conda environment from scratch

#82 marinak-ebi closed 1 month ago
1
Write script to access `Applied method` field in old releases in `scripts` folder with helper scripts

#81 marinak-ebi closed 2 months ago
0
Write script to access `Applied method` field of the statistical results for old releases

#80 marinak-ebi closed 2 months ago
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v2.0.1: EYE data bug fix

#79 marinak-ebi closed 2 months ago
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Update mapping files for ocular phenotypes

#78 marinak-ebi closed 2 months ago
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Ocular phenotypes LA data still go through the analysis

#77 marinak-ebi opened 4 months ago
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[EYE Analysis] Create test datasets for LA EYE data issue

#76 ficolo closed 4 months ago
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Remove unused code

#75 marinak-ebi opened 5 months ago
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v2.0.0: SLURM pipeline

#74 marinak-ebi closed 5 months ago
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Update instructions for running on SLURM

#73 marinak-ebi closed 5 months ago
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Refactor how `mp_chooser` file is specified

#72 marinak-ebi closed 5 months ago
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Refactor how `mp_chooser` file is specified

#71 marinak-ebi closed 5 months ago
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Update `CategoryMap.conf` for renaming categories

#70 marinak-ebi closed 5 months ago
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Update `CategoryMap.conf` for renaming categories

#69 marinak-ebi closed 5 months ago
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Streamline `mp_chooser` file naming

#68 marinak-ebi closed 5 months ago
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Fix logs of annotation pipeline

#67 marinak-ebi closed 5 months ago
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Remove duplications of `CategoryRemapping.tsv`

#66 marinak-ebi opened 5 months ago
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Fix error during gross morphology data analysis

#65 marinak-ebi closed 5 months ago
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Create function `submit_limit_jobs` that limit number of submitted job

#64 marinak-ebi closed 5 months ago
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Migrate all pipelines from LSF to SLURM

#63 marinak-ebi closed 5 months ago
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v1.0.0: Stable LSF pipeline

#62 marinak-ebi closed 5 months ago
0
[EYE Data] ‘No data’ categories count towards abnormal phenotypes in the stats pipeline leading to incorrect calls

#61 ficolo closed 4 months ago
2
[Testing data] Provide testing data for Embryo gross morphology parameters

#60 ficolo closed 5 months ago
0
[Testing data] Provide a testing dataset for the EYE LA data category collapsing issue

#59 ficolo closed 5 months ago
0
[Embryo] Gross morphology data shouldn't be analysed by the stats pipeline

#58 ficolo closed 5 months ago
4
Consider using SSD instead of HDD

#57 marinak-ebi opened 6 months ago
0
[Testing data] Provide a testing dataset for the low-n numbers lines / procedures

#56 ficolo closed 5 months ago
1
Create instructions for execution on SLURM

#55 marinak-ebi closed 5 months ago
0
Fix logs of annotation pipeline

#54 marinak-ebi closed 5 months ago
0
Update instructions

#53 marinak-ebi closed 5 months ago
0
Automatically check exit status of SLURM jobs

#52 marinak-ebi opened 6 months ago
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Measure execution time of annotation pipeline

#51 marinak-ebi opened 6 months ago
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Update LSF running instructions

#50 marinak-ebi closed 5 months ago
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Release stable LSF pipeline

#49 marinak-ebi closed 5 months ago
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Find out a way to limit number of submitted job on phase III

#48 marinak-ebi closed 5 months ago
0
Remove multicore initialisation and address `serverSocket` Error

#47 marinak-ebi closed 6 months ago
1
Enhance MP term field

#45 marinak-ebi opened 6 months ago
0