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Import metadata, counts api#133

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myushen wants to merge 41 commits intostemangiola:masterstemangiola/CuratedAtlasQueryR:masterfrom myushen:import-apimyushen/CuratedAtlasQueryR:import-apiCopy head branch name to clipboard

+399-88

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Commits on Feb 28, 2024

• export default_cache function, add clear_cache function

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  9a2b287

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Commits on Mar 1, 2024

• check metadata, gene names, positive counts, file_id

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• generate cpm from original, check subdir number match

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• check metadata input has minimum set of column names and types

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Commits on Mar 4, 2024

• add check age, sex, minimum sets of input columns

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  1b0d608

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• upload meta, counts to cloud

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• add documentation

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• Revert "upload meta, counts to cloud"

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• add function import_metadata_counts

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Commits on Mar 5, 2024

• fix

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  0e5e27c

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• try fix code suggested by knitr error

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• Revert "try fix code suggested by knitr error"

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Commits on Mar 6, 2024

• remove meta_output argument, add counts_path argument

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• add counts_per_million function

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  bf8aa68

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• fix error

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  56c32ea

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• fix memory issue in counts_per_million

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  593dcc7

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• fix documentation

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  815648c

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• add check: cells_ cannot be duplicates when join with api

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Commits on Mar 7, 2024

• add checkpoint, cell_ values in metadata must be unique

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Commits on Mar 8, 2024

• optimise code and comments

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  1fdea73

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• fix tiny issue

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• assert_that

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Commits on Mar 12, 2024

• read rds, assign matrix for counts data, save HDF5

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• accept sce RDS as input

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Commits on Mar 13, 2024

• accept count_path_df.rds as an input

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  1c4aa79

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• roxygenise

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  f8bda0b

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• fix a missing variable

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  8e34280

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• tiny fix

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  bdf294b

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• checking whether gene set of new count data and old count data match

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Commits on Mar 14, 2024

• change function input, accept sce rds and cache dir only

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  77d0b68

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• fix a variable

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• save created file_id_db column in metadata slot to rds

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  2ab8a45

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• fix variable

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  97cbfa5

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Commits on Mar 15, 2024

• accept a loaded sce_obj as input

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Commits on Mar 18, 2024

• checking whether genes in a list of SCEs overlap

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• use gene intersection if genes across SCEs do not completely overlap

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Commits on Mar 19, 2024

• move check_gene_overlap function to counts.R

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  15628a4

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• optimise counts_per_million.R. interact import API with get_SCE

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  8e2c89c

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• change function documentation

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  2792f11

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• fix assert_that

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  1209f7c

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• update Rd and local checks

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