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gn-uploader: Data uploader for GeneNetwork
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12 days
Fix linting and typing errors.
Frederick Muriuki Muriithi
2024-10-21
Add utilities for reading text files and csv files
Frederick Muriuki Muriithi
2024-10-17
Ignore comment lines.
Frederick Muriuki Muriithi
2024-10-14
Update typing information.
Frederick Muriuki Muriithi
2024-10-14
Improve error messages for R/qtl2 code.
Frederick Muriuki Muriithi
2024-08-28
Fix imports, and minor bugs.
Frederick Muriuki Muriithi
2024-08-12
Bug: Ensure file type values are lists.
Frederick Muriuki Muriithi
2024-08-12
Update check for missing files: Check from directory.
Frederick Muriuki Muriithi
2024-08-12
Add utility to transpose CSVs, renaming the original file.
Frederick Muriuki Muriithi
2024-08-12
Define new InvalidValue error type.
Frederick Muriuki Muriithi
2024-08-12
Rename module: Module contains exceptions classes.
Frederick Muriuki Muriithi
2024-08-09
Read R/qtl2 control data from a directory with extracted files.
Frederick Muriuki Muriithi
2024-08-08
Function to transpose CSV files.
Frederick Muriuki Muriithi
2024-08-08
Add utility function to extract R/qtl2 zip bundles
Frederick Muriuki Muriithi
2024-06-20
Check for special files that might share names/extensions
Frederick Muriuki Muriithi
2024-02-21
Check that samples/cases are consistent
Frederick Muriuki Muriithi
2024-02-20
Track filename in the errors
Frederick Muriuki Muriithi
2024-02-20
Generalise fetching of samples/cases/individuals.
Frederick Muriuki Muriithi
2024-02-20
Read samples from geno file.
Frederick Muriuki Muriithi
2024-02-20
Read each file separately
Frederick Muriuki Muriithi
2024-02-20
Stand-alone function to read control file
Frederick Muriuki Muriithi
2024-02-16
Replace genotype codes with values in control file.
Frederick Muriuki Muriithi
2024-02-16
Convert missing value codes to None
Frederick Muriuki Muriithi
2024-02-16
Strip comment lines.
Frederick Muriuki Muriithi
2024-02-16
Read raw text data from a file in the zip bundle
Frederick Muriuki Muriithi
2024-02-13
Make "FILE_TYPES" part of public interface for module/package.
Frederick Muriuki Muriithi
2024-02-12
Refactor: Use new decimal places checker.
Frederick Muriuki Muriithi
2024-02-12
Check for errors in the 'phenose' file.
Frederick Muriuki Muriithi
2024-02-12
Provide the key for each file listed in the control file.
Frederick Muriuki Muriithi
2024-02-08
Generalise error retrieval: extract common structure
Frederick Muriuki Muriithi
2024-02-08
Use error objects rather than plain tuple values.
Frederick Muriuki Muriithi
2024-02-06
Check that pheno values are numerical and at least 3 decimal places
Frederick Muriuki Muriithi
2024-02-05
Check that data in geno file is valid
Frederick Muriuki Muriithi
2024-02-05
Fix linting and type errors.
Frederick Muriuki Muriithi
2024-02-05
Do general bundle validation and show errors
Frederick Muriuki Muriithi
2024-02-05
Retrieve list of all files, and list of missing files
Frederick Muriuki Muriithi
2024-02-02
List file types in a single place for easier reuse
Frederick Muriuki Muriithi
2024-02-02
Ensure control file defaults are set up in code.
Frederick Muriuki Muriithi
2024-01-16
Provide defaults for various control variables
Frederick Muriuki Muriithi
2024-01-15
Process `na.strings` even for default cases
Frederick Muriuki Muriithi
2024-01-15
Extract common functional tools to separate package.
Frederick Muriuki Muriithi
2024-01-10
Provide convenience functions to avoid subtle call errors
Frederick Muriuki Muriithi
2024-01-10
Make identifier column name explicit
Frederick Muriuki Muriithi
2024-01-09
Raise exception on reading non-existing file
Frederick Muriuki Muriithi
2024-01-08
Upload R/qtl2 zip bundle and check for errors.
Frederick Muriuki Muriithi
2024-01-04
Parse sex information from R/qtl bundle.
Frederick Muriuki Muriithi
2024-01-04
Parse cross information from R/qtl2 bundle.
Frederick Muriuki Muriithi
2024-01-04
Process sex and cross information data in "covar" files.
Frederick Muriuki Muriithi
2024-01-04
Parse multiple files with same file key.
Frederick Muriuki Muriithi
2024-01-03
Use generic parser. Remove obsoleted functions.
Frederick Muriuki Muriithi
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