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module data input #74

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module data input #74

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myushen
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@myushen myushen commented Jul 30, 2024

  • enabling gene nomenclature option in the pipeline
  • fixing functions for anndata input

myushen added 9 commits July 15, 2024 17:38
@myushen
update functions for anndata input work
5029672
@myushen
update module for anndata/sce input
3b2e1d4
@myushen
merge, solve conflicts from master
6591188 
Merge branch 'master' into module-data-input

Conflicts:
	R/functions.R
	R/modules_grammar_hpc.R
@myushen
fix
09baa87
@myushen
fix package dependency
2d78027
@myushen
fix mt-ribsome gene identification and pipeline running
f2087a8
@myushen
fix
ce36536
@myushen
merge from master
289a037 
Merge branch 'master' into module-data-input

Conflicts:
	tests/testthat/test_single_functions.R
@myushen
Squashed commit of the following:
a480073 
commit 44a9103
Author: Mengyuan Shen <[email protected]>
Date:   Thu Aug 15 10:32:04 2024 +1000

    update transformation function

commit ef88d91
Author: myushen <[email protected]>
Date:   Wed Aug 14 19:19:11 2024 +1000

    update transformation function

commit 3d6d946
Author: myushen <[email protected]>
Date:   Wed Aug 14 17:04:48 2024 +1000

    testthat for census data

commit f393990
Author: myushen <[email protected]>
Date:   Fri Aug 9 17:30:34 2024 +1000

    fix the pipeline for census anndata input

commit eff84af
Author: myushen <[email protected]>
Date:   Tue Aug 6 14:35:27 2024 +1000

    fix pipeline

commit e8c56ad
Author: myushen <[email protected]>
Date:   Mon Aug 5 15:44:16 2024 +1000

    save transform assay in different formats

commit 157d6dc
Merge: 289a037 188f0b5
Author: myushen <[email protected]>
Date:   Mon Aug 5 11:21:17 2024 +1000

    fix conflicts

    Merge remote-tracking branch 'remotes/upstream/custom_input_names' into transform-assays

    Conflicts:
    	R/functions.R
    	R/modules_grammar_hpc.R
    	tests/testthat/test_single_functions.R

commit 188f0b5
Author: stemangiola <[email protected]>
Date:   Mon Aug 5 00:49:11 2024 +1000

    update output names

commit 52c0e73
Author: stemangiola <[email protected]>
Date:   Sun Aug 4 23:48:02 2024 +1000

    SCT delay array

commit bb4ca16
Author: stemangiola <[email protected]>
Date:   Sun Aug 4 19:10:20 2024 +1000

    add list of functions

commit 80cf0c2
Author: stemangiola <[email protected]>
Date:   Sun Aug 4 17:53:28 2024 +1000

    fix argument

commit 0412643
Author: stemangiola <[email protected]>
Date:   Sun Aug 4 17:49:43 2024 +1000

    fix output names setting

commit b4003b7
Author: stemangiola <[email protected]>
Date:   Sun Aug 4 14:34:39 2024 +1000

     fix DE

commit 50a1a5d
Author: stemangiola <[email protected]>
Date:   Sun Aug 4 11:29:39 2024 +1000

    fixed custom input for some functions

commit a9f89e6
Merge: 78b5553 05b75d2
Author: stemangiola <[email protected]>
Date:   Sat Aug 3 00:01:00 2024 +1000

    Merge branch 'master' into custom_input_names

commit 05b75d2
Author: stemangiola <[email protected]>
Date:   Sat Aug 3 00:00:19 2024 +1000

    intentate

commit 78b5553
Author: stemangiola <[email protected]>
Date:   Fri Aug 2 22:49:58 2024 +1000

    make input target dynamic
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@myushen