loomr.git
4 months agoAdd license master
Marcel Schilling [Sat, 24 Nov 2018 19:39:18 +0000 (20:39 +0100)]
Add license

* GPL-3 was indicated in `DESCRIPTION`.
* Copyright was assigned based on git log.

17 months agoUpdate DESCRIPTION
Paul Hoffman [Wed, 25 Apr 2018 14:38:15 +0000 (10:38 -0400)]
Update DESCRIPTION

17 months agoUpdate README 0.2.0-beta
Paul Hoffman [Mon, 23 Apr 2018 22:15:22 +0000 (18:15 -0400)]
Update README

17 months agoUpdate to 0.2.0
Paul Hoffman [Mon, 23 Apr 2018 22:11:50 +0000 (18:11 -0400)]
Update to 0.2.0

17 months agoMinor fixes to documentation
Paul Hoffman [Mon, 23 Apr 2018 22:11:18 +0000 (18:11 -0400)]
Minor fixes to documentation

17 months agoUpdate documentation
Paul Hoffman [Sun, 22 Apr 2018 23:27:02 +0000 (19:27 -0400)]
Update documentation

17 months agoMerge branch 'develop' of github.com:mojaveazure/loomR into develop
Paul Hoffman [Sun, 22 Apr 2018 20:19:40 +0000 (16:19 -0400)]
Merge branch 'develop' of github.com:mojaveazure/loomR into develop

17 months agoUpdate documentation
Paul Hoffman [Sun, 22 Apr 2018 20:19:32 +0000 (16:19 -0400)]
Update documentation

17 months agoAdd calc.numi option to create
Paul Hoffman [Sun, 22 Apr 2018 20:19:26 +0000 (16:19 -0400)]
Add calc.numi option to create

17 months agominor fixes in combine to handle multiple col attrs
andrewwbutler [Wed, 18 Apr 2018 21:04:42 +0000 (17:04 -0400)]
minor fixes in combine to handle multiple col attrs

17 months agoFix combine to take a list instead of a vector
Paul Hoffman [Wed, 18 Apr 2018 15:06:00 +0000 (11:06 -0400)]
Fix combine to take a list instead of a vector
Allows combining loom objects instead of/in addition to paths to loom files

17 months agoUpdate .gitignore
Paul Hoffman [Wed, 18 Apr 2018 15:05:18 +0000 (11:05 -0400)]
Update .gitignore

18 months agoSpeed improvements to subset.loom
Paul Hoffman [Thu, 5 Apr 2018 15:28:52 +0000 (11:28 -0400)]
Speed improvements to subset.loom

18 months agoUpdate documentation
Paul Hoffman [Tue, 3 Apr 2018 20:18:43 +0000 (16:18 -0400)]
Update documentation

18 months agoChanges to loom$map to (hopefully) speed up chunking data with selected indices
Paul Hoffman [Tue, 3 Apr 2018 20:18:28 +0000 (16:18 -0400)]
Changes to loom$map to (hopefully) speed up chunking data with selected indices

18 months agoAutomatically sort index.use in apply
Paul Hoffman [Tue, 27 Mar 2018 15:12:58 +0000 (11:12 -0400)]
Automatically sort index.use in apply

18 months agoFix graph validation in validateLoom
Paul Hoffman [Mon, 26 Mar 2018 22:07:12 +0000 (18:07 -0400)]
Fix graph validation in validateLoom

18 months agoAdd graph validation step
Paul Hoffman [Mon, 26 Mar 2018 21:36:01 +0000 (17:36 -0400)]
Add graph validation step

18 months agoChange apply to load all data, then subset rather than read non-consecutive indices...
Paul Hoffman [Mon, 26 Mar 2018 20:45:35 +0000 (16:45 -0400)]
Change apply to load all data, then subset rather than read non-consecutive indices, minor fix to add.graph

18 months agoAdd preliminary graph support
Paul Hoffman [Mon, 26 Mar 2018 15:10:10 +0000 (11:10 -0400)]
Add preliminary graph support

18 months agoset stringsAsFactors = FALSE in get.attribute.df
Christoph Hafemeister [Wed, 21 Mar 2018 21:51:12 +0000 (22:51 +0100)]
set stringsAsFactors = FALSE in get.attribute.df

18 months agoModify get.attribute.df to return all attributes by default and to skip all 2D attributes
Christoph Hafemeister [Wed, 21 Mar 2018 21:37:27 +0000 (22:37 +0100)]
Modify get.attribute.df to return all attributes by default and to skip all 2D attributes

18 months agoHave create, combine, and subset.loom automatically create graph groups instead of...
Paul Hoffman [Wed, 21 Mar 2018 19:33:01 +0000 (15:33 -0400)]
Have create, combine, and subset.loom automatically create graph groups instead of edge groups

18 months agoAdd validation for graphs
Paul Hoffman [Wed, 21 Mar 2018 19:28:19 +0000 (15:28 -0400)]
Add validation for graphs

18 months agoRemove redundant code
Paul Hoffman [Wed, 21 Mar 2018 18:15:55 +0000 (14:15 -0400)]
Remove redundant code

18 months agoBug fix in subset.loom
Paul Hoffman [Tue, 20 Mar 2018 22:51:27 +0000 (18:51 -0400)]
Bug fix in subset.loom

18 months agoFixes to apply, field loading, and subset.loom; new update.shape method
Paul Hoffman [Mon, 19 Mar 2018 20:50:33 +0000 (16:50 -0400)]
Fixes to apply, field loading, and subset.loom; new update.shape method

18 months agoChanges to warning messages in create
Paul Hoffman [Mon, 19 Mar 2018 15:33:45 +0000 (11:33 -0400)]
Changes to warning messages in create

18 months agoProvide S4 Matrix methods to loomR for data manipulation
Paul Hoffman [Mon, 19 Mar 2018 14:42:43 +0000 (10:42 -0400)]
Provide S4 Matrix methods to loomR for data manipulation

18 months agoFixes to loom$apply and subset.loom
Paul Hoffman [Fri, 16 Mar 2018 23:18:31 +0000 (19:18 -0400)]
Fixes to loom$apply and subset.loom

18 months agoMinor fix in loom
Paul Hoffman [Fri, 16 Mar 2018 20:29:24 +0000 (16:29 -0400)]
Minor fix in loom

19 months agoUpdate documentation, change the way apply creates datasets
Paul Hoffman [Thu, 15 Mar 2018 15:09:01 +0000 (11:09 -0400)]
Update documentation, change the way apply creates datasets

19 months agoUpdate documentation
Paul Hoffman [Wed, 14 Mar 2018 17:55:46 +0000 (13:55 -0400)]
Update documentation

19 months agoShow link for subset.loom when calling help on subset
Paul Hoffman [Wed, 14 Mar 2018 17:55:38 +0000 (13:55 -0400)]
Show link for subset.loom when calling help on subset

19 months agoTweaks to catn
Paul Hoffman [Wed, 14 Mar 2018 17:55:04 +0000 (13:55 -0400)]
Tweaks to catn

19 months agoAdd ability to transpose input data
Paul Hoffman [Thu, 8 Mar 2018 23:54:07 +0000 (18:54 -0500)]
Add ability to transpose input data

19 months agoUpdate README
Paul Hoffman [Thu, 8 Mar 2018 23:53:54 +0000 (18:53 -0500)]
Update README

19 months agoMerge branch 'master' into develop
Paul Hoffman [Mon, 5 Mar 2018 23:03:49 +0000 (18:03 -0500)]
Merge branch 'master' into develop

19 months agoAdd loomR::combine
Paul Hoffman [Thu, 1 Mar 2018 00:35:51 +0000 (19:35 -0500)]
Add loomR::combine

19 months agoUpate documentation
Paul Hoffman [Thu, 1 Mar 2018 00:35:37 +0000 (19:35 -0500)]
Upate documentation

19 months agoMore updates
Paul Hoffman [Wed, 28 Feb 2018 23:22:18 +0000 (18:22 -0500)]
More updates

19 months agoUpdates to gitignore and DESCRIPTION
Paul Hoffman [Wed, 28 Feb 2018 16:14:31 +0000 (11:14 -0500)]
Updates to gitignore and DESCRIPTION

19 months agoMerge branch 'develop' of github.com:mojaveazure/loomR into develop
Paul Hoffman [Tue, 27 Feb 2018 23:50:20 +0000 (18:50 -0500)]
Merge branch 'develop' of github.com:mojaveazure/loomR into develop

19 months agoStart working on a combine function
Paul Hoffman [Tue, 27 Feb 2018 23:50:10 +0000 (18:50 -0500)]
Start working on a combine function

19 months agoMinor usability fix
Paul Hoffman [Fri, 23 Feb 2018 23:49:39 +0000 (18:49 -0500)]
Minor usability fix

19 months agoMerge branch 'develop' of github.com:mojaveazure/loomR into develop
Andrew Butler [Fri, 23 Feb 2018 19:46:08 +0000 (14:46 -0500)]
Merge branch 'develop' of github.com:mojaveazure/loomR into develop

19 months agoclose progress bar connections
Andrew Butler [Fri, 23 Feb 2018 19:45:43 +0000 (14:45 -0500)]
close progress bar connections

19 months agoChange validation to add missing groups; update documentation
Paul Hoffman [Thu, 22 Feb 2018 23:21:43 +0000 (18:21 -0500)]
Change validation to add missing groups; update documentation

19 months agoAdd preliminary support for row and column edges
Paul Hoffman [Wed, 21 Feb 2018 23:24:09 +0000 (18:24 -0500)]
Add preliminary support for row and column edges

20 months agoallow add.attribute to take a data.frame - convert to named list
andrewwbutler [Fri, 9 Feb 2018 19:43:20 +0000 (14:43 -0500)]
allow add.attribute to take a data.frame - convert to named list

20 months agoUpdate documentation some more
Paul Hoffman [Fri, 9 Feb 2018 03:12:25 +0000 (22:12 -0500)]
Update documentation some more

20 months agoUpdate documentation
Paul Hoffman [Fri, 9 Feb 2018 02:59:15 +0000 (21:59 -0500)]
Update documentation

20 months agoChange add.layers to support streaming sparse matrices
Paul Hoffman [Fri, 9 Feb 2018 02:58:54 +0000 (21:58 -0500)]
Change add.layers to support streaming sparse matrices

20 months agoFix documentation, add proper support for R sparse matrices
Paul Hoffman [Thu, 8 Feb 2018 15:34:29 +0000 (10:34 -0500)]
Fix documentation, add proper support for R sparse matrices

20 months agoremove extra comma, rerun docs
andrewwbutler [Wed, 7 Feb 2018 22:46:01 +0000 (17:46 -0500)]
remove extra comma, rerun docs

20 months agoChunk loomR::create
Paul Hoffman [Wed, 7 Feb 2018 22:38:51 +0000 (17:38 -0500)]
Chunk loomR::create

20 months agoMerge branch 'develop' of github.com:mojaveazure/loomR into develop
Paul Hoffman [Wed, 31 Jan 2018 00:03:36 +0000 (19:03 -0500)]
Merge branch 'develop' of github.com:mojaveazure/loomR into develop

20 months agoAdd support for multidimensional row- and column-attributes
Paul Hoffman [Wed, 31 Jan 2018 00:03:30 +0000 (19:03 -0500)]
Add support for multidimensional row- and column-attributes

20 months agoMerge pull request #4 from ChristophH/master
Paul Hoffman [Tue, 30 Jan 2018 22:51:33 +0000 (17:51 -0500)]
Merge pull request #4 from ChristophH/master

fix bug in create when checking chunk.dims length

20 months agoMerge pull request #5 from ChristophH/develop
Paul Hoffman [Tue, 30 Jan 2018 22:50:50 +0000 (17:50 -0500)]
Merge pull request #5 from ChristophH/develop

more flexible handling of result matrices when mapping functions

20 months agoallow more flexible results shapes when mapping a function
Christoph Hafemeister [Tue, 30 Jan 2018 22:40:03 +0000 (23:40 +0100)]
allow more flexible results shapes when mapping a function

20 months agoMerge branch 'master' into develop
Christoph Hafemeister [Tue, 30 Jan 2018 21:45:39 +0000 (22:45 +0100)]
Merge branch 'master' into develop

21 months agofix bug in create when checking chunk.dims length
ChristophH [Tue, 9 Jan 2018 12:43:09 +0000 (13:43 +0100)]
fix bug in create when checking chunk.dims length

21 months agoUse logging functions, change error messages, expand add.loom
Paul Hoffman [Wed, 3 Jan 2018 22:47:36 +0000 (17:47 -0500)]
Use logging functions, change error messages, expand add.loom

21 months agoAdd some new logging functions
Paul Hoffman [Wed, 3 Jan 2018 22:46:50 +0000 (17:46 -0500)]
Add some new logging functions

21 months agoFixes to add.cells, start add.loom
Paul Hoffman [Wed, 3 Jan 2018 19:54:13 +0000 (14:54 -0500)]
Fixes to add.cells, start add.loom

21 months agoMinor fix to subset.loom, added more to add.cells
Paul Hoffman [Tue, 2 Jan 2018 23:58:25 +0000 (18:58 -0500)]
Minor fix to subset.loom, added more to add.cells
Adding cells should work, haven't tested it yet so I can't say for sure

21 months agoAdd stuff for add.cells
Paul Hoffman [Tue, 19 Dec 2017 22:23:47 +0000 (14:23 -0800)]
Add stuff for add.cells

22 months agoFix display messages
Paul Hoffman [Wed, 13 Dec 2017 20:47:57 +0000 (15:47 -0500)]
Fix display messages

22 months agoMade changes and tested them, subset.loom works now (or in my one test it does)
Paul Hoffman [Wed, 13 Dec 2017 20:17:03 +0000 (15:17 -0500)]
Made changes and tested them, subset.loom works now (or in my one test it does)

22 months agoR doesn't evaluate variables in list creation...
Paul Hoffman [Wed, 13 Dec 2017 19:44:31 +0000 (14:44 -0500)]
R doesn't evaluate variables in list creation...

22 months agoI should fix create at some point...
Paul Hoffman [Wed, 13 Dec 2017 19:35:24 +0000 (14:35 -0500)]
I should fix create at some point...

22 months agoIf you're happy and you know it, syntax error!
Paul Hoffman [Wed, 13 Dec 2017 19:32:44 +0000 (14:32 -0500)]
If you're happy and you know it, syntax error!

22 months agoBecause I can't remember how my methods work...
Paul Hoffman [Wed, 13 Dec 2017 19:26:05 +0000 (14:26 -0500)]
Because I can't remember how my methods work...

22 months agoBug fix in create
Paul Hoffman [Wed, 13 Dec 2017 19:15:41 +0000 (14:15 -0500)]
Bug fix in create

22 months agoAdd some defaults to subset.loom
Paul Hoffman [Wed, 13 Dec 2017 19:06:23 +0000 (14:06 -0500)]
Add some defaults to subset.loom

22 months agoUpdate author list
Paul Hoffman [Wed, 13 Dec 2017 19:06:13 +0000 (14:06 -0500)]
Update author list

22 months agoUpdate description
Paul Hoffman [Wed, 13 Dec 2017 00:13:11 +0000 (19:13 -0500)]
Update description

22 months agoCleanup and reorganize code
Paul Hoffman [Wed, 13 Dec 2017 00:05:12 +0000 (19:05 -0500)]
Cleanup and reorganize code

22 months agoAdd subset function
Paul Hoffman [Tue, 12 Dec 2017 23:57:18 +0000 (18:57 -0500)]
Add subset function

22 months agoBegan support for selective-chunking in apply
Paul Hoffman [Tue, 12 Dec 2017 23:01:02 +0000 (18:01 -0500)]
Began support for selective-chunking in apply

22 months agoSlight refactoring
Paul Hoffman [Tue, 12 Dec 2017 18:58:26 +0000 (13:58 -0500)]
Slight refactoring

22 months agoadd ability to extract a dataframe of multiple row_attr or col_attr elements
Andrew Butler [Tue, 12 Dec 2017 15:29:26 +0000 (10:29 -0500)]
add ability to extract a dataframe of multiple row_attr or col_attr elements

22 months agoFixes to batch iteration. Allow skipping of validation due to issues with large datasets
Paul Hoffman [Thu, 16 Nov 2017 00:17:24 +0000 (19:17 -0500)]
Fixes to batch iteration. Allow skipping of validation due to issues with large datasets

22 months agoSyntax error
Paul Hoffman [Wed, 15 Nov 2017 21:21:09 +0000 (16:21 -0500)]
Syntax error

22 months agoBeginnings of add cells method
Paul Hoffman [Tue, 14 Nov 2017 22:56:41 +0000 (17:56 -0500)]
Beginnings of add cells method

23 months agoSyntax error
Paul Hoffman [Tue, 14 Nov 2017 20:00:35 +0000 (15:00 -0500)]
Syntax error

23 months agoMerge branch 'master' of github.com:mojaveazure/loomR
Paul Hoffman [Tue, 14 Nov 2017 19:19:54 +0000 (14:19 -0500)]
Merge branch 'master' of github.com:mojaveazure/loomR

23 months agoUse characters rather than 'versions' to store version information
Paul Hoffman [Tue, 14 Nov 2017 15:24:37 +0000 (10:24 -0500)]
Use characters rather than 'versions' to store version information

23 months agoAdd method to clean up object once garbage collected
Paul Hoffman [Thu, 9 Nov 2017 23:04:00 +0000 (18:04 -0500)]
Add method to clean up object once garbage collected

23 months agoUpdate README.md
Paul Hoffman [Thu, 9 Nov 2017 20:16:37 +0000 (15:16 -0500)]
Update README.md

23 months agoUpdate documentation
Paul Hoffman [Thu, 9 Nov 2017 19:29:28 +0000 (14:29 -0500)]
Update documentation

23 months agoFixed issues with chunking and iterating
Paul Hoffman [Thu, 9 Nov 2017 18:27:23 +0000 (13:27 -0500)]
Fixed issues with chunking and iterating

23 months agoUpdate issues with chunk iteration
Paul Hoffman [Thu, 9 Nov 2017 17:27:05 +0000 (12:27 -0500)]
Update issues with chunk iteration

23 months agoFix issue with adding attributes
Paul Hoffman [Thu, 9 Nov 2017 17:19:38 +0000 (12:19 -0500)]
Fix issue with adding attributes

23 months agoAdd overwrite to add layer and add atribute
Paul Hoffman [Thu, 9 Nov 2017 17:14:25 +0000 (12:14 -0500)]
Add overwrite to add layer and add atribute

23 months agochange margin to 1 for genes and 2 for cells
Paul Hoffman [Thu, 9 Nov 2017 16:31:24 +0000 (11:31 -0500)]
change margin to 1 for genes and 2 for cells

23 months agoupdate readme
Paul Hoffman [Wed, 8 Nov 2017 21:41:52 +0000 (16:41 -0500)]
update readme

23 months agoCleanup namespace
Paul Hoffman [Wed, 8 Nov 2017 13:54:52 +0000 (08:54 -0500)]
Cleanup namespace

23 months agoClean code
Paul Hoffman [Wed, 8 Nov 2017 00:58:07 +0000 (19:58 -0500)]
Clean code