bug fix in hexbin coords
 

 added areas for bins
 

 bump version to 1.1.1
 

 fix Docs
 

 add code notes
 

 use R-release
 

 Improved usability of the method `storeGDI()` (#81)

Now the method `storeGDI()` can take in the output `data.frame`
from the function `calculateGDI()`

Co-authored-by: Silvia Giulia Galfre <49807846+seriph78@users.noreply.github.com> 

 fix vign01
 

 update to bioc 3.19, man files more intuitive
 

 fixing method name reverse issue in test files
 

 Merge pull request #131 from PhanstielLab/maintainer_devel

Updating maintainers (devel) 

 Updating tests
 

 bump version
 

 merge PR #61

Merge branch 'main' of https://github.com/zellerivo/DEGreport into zellerivo-main

# Conflicts:
#	R/clustering.R
 

 update comments
 

 fix parameter
 

 remove fixed number of rows for facet plot
 

 remove x axis label
 

 changed the sequence of trajectory plots to match the sequence of clusters in the dendogram
 

 changes
 

 vignette updates
 

 Version bump
 

 Use devel branch in links 

 Merge pull request #16 from llrs/patch-3

Update link to singleR book 

 Minor fixes to documentation (#29)

 

 Change Daniel's email address
 

 update news, version bump
 

 tstats update

+ prevent dropping of columns
+ add control_group parameter
 

 update to use _PACKAGE for documentation
 

 fix the issue of reload everything when edit the cell info
 

 relax unit tests
 

 update author info; version bump 1.29.0>.1
 

 Updated to C++ 17
 

 update vignette with new methods "log10" (transformAssay) and "none" (imputeAssay)
 

 Update landingPage.R
 

 fix untarg data import

- remove unnecessary column by name instead of index
- prevent dropping of columns
 

 DMRcate_3.1.4
 

 fix classifier
 

 merge 3.6.3 changes
 

 some meaningful message
 

 minor whitespace and other cleanup

- move `clinvar_data()` definition above `clinvar_plot()` for man page
  collation
- add / update unit test for sql import templates
- version bump
 

 rename clinvar_plot* to ClinVar*

- contradicts PR review comment! (sorry)
- consistent with organization of other functions
 

 use `set_ht_opt`
 

 adjust `with_ht_verbose` and `with_ht_opts`
 

 Adding feature colname attribute.
 

 add single click to remove the editor box.
 

 eval=FALSE a demo block
 

 updated vignette (still need to add MHT section)
 

 change output column name
 

 change the output column name
 

 change the output column name
 

 fix unit tests, use terminal nodes only
 

 Add get_terminal_nodes function. Will be useful for avoiding multicollinearity in datasets with synthetic nodes.
 

 Implements MHT correction. Unit tests still need fixing. See #39.
 

 NEWS for the new release
 

 set version of scvelo triggering the deprecation error to 0.3.1 (#75)

Co-authored-by: Kevin Rue <kevinrue@users.noreply.github.com> 

 fix Docs
 

 better Docs style
 

 hide the layout preparing methods
 

 Added SCEtoSeurat export to NAMESPACE
 

 Resolve merge conflicts and merge 'bioconductor/devel' into 'devel'
 

 Correct spelling errors in vignette
 

 base on bioc comments
 

 fixing bug, updating the vignettes, dropping expData file in data dir
 

 bug fix: make annotation column class to character
 

 add suffix removal support to DMR
 

 use gitignore to filter out false positives
 

 Version bump
 

 Add missing @ to link to the Clustring pacakge 

 version bump, NEWS update; add @tram-nguyen-n as author
 

 edit `clinvar_plot()` so it will work with `clinvar_data$label` "benign" and "pathogenic".
 

 Merge pull request #3 from ccb-hms/martins_fixes

Merge additional fixes from Martin 

 return clinvar_table as tibble
 

 roxygen links for tibble data.frame
 

 lynx to `browseURL()` for downloading
 

 nrow to NROW
 

 bumped version
 

 Updated test cases to reflect changes in `clinvar_plot()`
- removed any function relevant for printing and evaluating Messages since `clinvar_plot()` now uses spdl::info
- suppressed warning from dplyr for testing about outdated versioning
 

 removed LazyData from DESCRIPTION because clinvar_data is no longer in-house data
 

 quote around column names
 

 formatting
 

 edited documentation for `clinvar_data()` to describe raw supplemental table that is loaded from database
 

 renamed `test-clinvar_plot` file and updated function names within file
 

 - loading in clinvar data from database with `clinvar_data()` in `clinvar_filter_cv_table` helper function
- removed clinvar processing from `make_clinvar_dataset.R` and included it as part of `clinvar_filter_cv_table` instead
 

 Edits to script for obtaining ClinVar data from AM paper Supplement.
- replaced `wget` solution with `lynx` option `-accept_all_cookies=TRUE` in order to bypass 403 ERROR Status
- used `unzip()` and `R.utils::gzip()` as an R solution
- removed `usethis::use_data()` command since clinvar_data is no longer hosted in-package
 

 changed delim so that it will accept delim parameter passed by user in the function `am_data_import_csv()`. Needed for correctly loading the `clinvar_data()` DuckDB table
 

 formatting: variable assignment separate from the transformation stanza
 

 removed comment header
 

 edits to `clinvar_plot.R` and man `ClinVar.Rd`
- small syntax fixes
- helper and function naming convention following `clinvar_` prefix
 

 plotting functions and clinvar_data documentation to a single file `ClinVar.R`
 

 renamed `plot_clinvar` to `clinvar_plot`
 

 Changes suggested by Martin
 

 removed `LazyData: true`

- as suggested by BiocCheck
 

 R (>= 4.1.0) to Depends
 

 removed extra spaces
 

 Fix indentation
 

 wrapped one line > 80 characters
 

 removed @noRd from `plot_clinvar.R`

- devtools::document() returned "@noRd must not be followed by any text."
 

 minor edits to `plot_clinvar.R`

- Since user-defined table does not include lazy tbl, collect() will not work in this case. Therefore, `dplyr::collect()` back to `dplyr::tibble`
 

 Merge pull request #1 from ccb-hms/nt_fixes

Multiple fixes 

 changed helper function name from `.check_am_table` to `.load_am_table` which is more reflective of the function
 

 changed link for tibble and data.frame doc
 

 formatting to adhere to 4 spaces
 

 formatting and minor typos
 

 Helper functions for `plot_clinvar.R`
-functionality to check and load AlphaMissense and ClinVar tables.
- wrapped code to join, munge, and process AM and CV tables for plotting in helper function
- wrapped ggplot code for plotting and formatting in helper function
 

 Make minor changes to plot clinvar formatting
 

 removed indent from line 125 that was not 4 spaces
 

 utils,data to NAMESPACE

- to resolve NOTE:
plot_clinvar: no visible global function definition for ‘data’
   Undefined global functions or variables:
     data
 

 Edits to plot_clinvar.R file.
- use the `.data$` tidyselect syntax.
- Wrap and indent lines as needed.

Edits to plot_clinvar.Rd file.
- indentation
- documented dplyr::collect() change
 </pre>
    </div>
  
    

      Package: AlphaMissenseR

      Commit: 1c74b5693daaa7bde61a67f4591aed8ba277ee54

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-03 13:52:08 +0000

      Commit message:


	  
		
 Added `LazyData: true` to DESCRIPTION to assume resolving

- Warning: Variables with usage in Rd file 'clinvar_data.Rd' but not in code:
    ‘clinvar_data’
 
    
  
    

      Package: AlphaMissenseR

      Commit: 8c5a12c1b60ef9043cbb4e46ccf0e2a1b69fd943

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-03 13:26:32 +0000

      Commit message:


	  
		
 commented out usage.

- Following suggestion from:
https://stackoverflow.com/questions/57396392/warning-variables-with-usage-in-documentation-object-fang-but-not-in-code
 
    
  
    

      Package: AlphaMissenseR

      Commit: 0a514037f6fcdf55b4ee05b7865847f9ce316465

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-02 21:38:13 +0000

      Commit message:


	  
		
 Typo in YAML
 
    
  
    

      Package: AlphaMissenseR

      Commit: ce4c8468dbc464cefd43897737d9f6bd85577e9e

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-02 21:28:12 +0000

      Commit message:


	  
		
 Revised code to create `clinvar_data.rda` from compressed clinvar .csv.gz.

More informative name to `make_clinvar_dataset.R`
 
    
  
    

      Package: AlphaMissenseR

      Commit: 81bd26b14bb7bade4aedffa0c74cb6028c565d31

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-02 21:22:03 +0000

      Commit message:


	  
		
 gzipped clinvar .csv in inst/extdata to meet file size limit of 5 MB
 
    
  
    

      Package: AlphaMissenseR

      Commit: 30a1e71f3172ef2ed57de77dffdfa88cd8990cb2

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-02 21:20:43 +0000

      Commit message:


	  
		
 removed clinvar csv from inst/extdata due to size limit
 
    
  
    

      Package: AlphaMissenseR

      Commit: 952d92e9961130e4270df292eeb7bd22dc572231

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-02 14:43:44 +0000

      Commit message:


	  
		
 fixed tbl|data.frame validity check
 
    
  
    

      Package: AlphaMissenseR

      Commit: 1d7c50bbbf4aa43cc45cfc804b73a77b3cebfb27

      Author:  Nitesh Turaga <nitesh.turaga@gmail.com> 

      Date: 2024-05-01 12:12:24 -1000

      Commit message:


	  
		
 Edits to plot_clinvar.R file.

- use the `.data$` tidyselect syntax.
- Wrap and indent lines as needed.
- In the example, use dplyr::collect() instead of dplyr::as_tibble().

Edits to DATASET.R

- use `system.file()` for getting the file path of data.
- Use .data$ for tidyselection
- Use library calls for dplyr and tidyr.
 </pre>
    </div>
  
    

      Package: AlphaMissenseR

      Commit: bf3c49cb665855158844e072c02d30d9c501f811

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-01 20:44:34 +0000

      Commit message:


	  
		
 ggplot2 to Imports
 
    
  
    

      Package: AlphaMissenseR

      Commit: cff7ccdb6ca54889f28d7c308abbeb9d74e4aeaf

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-01 20:38:36 +0000

      Commit message:


	  
		
 ggplot2 to Suggests
 
    
  
    

      Package: AlphaMissenseR

      Commit: 9c8aa97f1b3623c5a76e00cfc3c76907ef37bdf4

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-01 20:37:57 +0000

      Commit message:


	  
		
 added sessionInfo
 
    
  
    

      Package: AlphaMissenseR

      Commit: 1509fc3f515d7ff92e199c22f0e7d98f3708e936

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-01 20:26:48 +0000

      Commit message:


	  
		
 removed plot P0DP23 as example
 
    
  
    

      Package: AlphaMissenseR

      Commit: adff30628817dc1c7fa255d101e1de6344099181

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-01 18:44:22 +0000

      Commit message:


	  
		
 typos
 
    
  
    

      Package: AlphaMissenseR

      Commit: 0e04ae2564020d9679a65ed5a9a05cf1c91e4b58

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-01 18:33:15 +0000

      Commit message:


	  
		
 changed r chunk names
 
    
  
    

      Package: AlphaMissenseR

      Commit: 0a80aec85723769a5320045bea305c7b677d79fc

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-01 17:59:47 +0000

      Commit message:


	  
		
 provided more info
 
    
  
    

      Package: AlphaMissenseR

      Commit: 7cc727caa694655ba6913b79de0f1f8bf708fd78

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-01 17:14:52 +0000

      Commit message:


	  
		
 renamed vignette
 
    
  
    

      Package: AlphaMissenseR

      Commit: d924f4cb3f6cc1c2e0dcd54c85232a6a291c3c7f

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-01 17:10:29 +0000

      Commit message:


	  
		
 formatting
 
    
  
    

      Package: AlphaMissenseR

      Commit: 82fb9720db25d2a5676965767664c1cba8f0dbaf

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-01 15:48:55 +0000

      Commit message:


	  
		
 table column info to details
 
    
  
    

      Package: AlphaMissenseR

      Commit: da0151a27aeb6fa16fcb0022d8cffdf1c85e2b91

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-05-01 15:17:06 +0000

      Commit message:


	  
		
 added plot legend and description
 
    
  
    

      Package: AlphaMissenseR

      Commit: 51e0889101dfc0e39f66ad49d254bcf9b1e74a31

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-04-25 21:06:06 +0000

      Commit message:


	  
		
 change function name in vignette
 
    
  
    

      Package: AlphaMissenseR

      Commit: 28e75f70ee6b7e7ec42184871b8e3add72d98d4c

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-04-25 21:05:53 +0000

      Commit message:


	  
		
 protein argument to uniprotId
 
    
  
    

      Package: AlphaMissenseR

      Commit: afca88424871c7a75e8bbf590fc4651a4fd767e4

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-04-25 17:31:10 +0000

      Commit message:


	  
		
 clinvar data out of global environment
 
    
  
    

      Package: AlphaMissenseR

      Commit: c5a01a775a78786f4e44eb10ab03529241f5e002

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-04-24 21:01:38 +0000

      Commit message:


	  
		
 renamed function
 
    
  
    

      Package: AlphaMissenseR

      Commit: bee63f0b56422008ffce2d26eaac4fee00cf0b06

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-04-23 19:22:14 +0000

      Commit message:


	  
		
 changed function name, added notes
 
    
  
    

      Package: AlphaMissenseR

      Commit: 6606d61a51741b52a52f944a9a4f5ceef6e1fb86

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-04-23 19:21:48 +0000

      Commit message:


	  
		
 changed title
 
    
  
    

      Package: AlphaMissenseR

      Commit: 6671d5e5d186172195b6e9bd0599d676f7d552ab

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-04-22 19:41:15 +0000

      Commit message:


	  
		
 cleaned up code. added comments with questions
 
    
  
    

      Package: AlphaMissenseR

      Commit: e7f0d077468b23ca0f62969f69c5de1d93aecd3e

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-04-22 14:35:09 +0000

      Commit message:


	  
		
 all tidyverse format
 
    
  
    

      Package: AlphaMissenseR

      Commit: 0c6adabf6a7a4e583de860244e5f944ff746cac1

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-04-22 13:48:09 +0000

      Commit message:


	  
		
 documentation for inhouse clinvar_data
 
    
  
    

      Package: AlphaMissenseR

      Commit: 437ddf2f5e4ba2f0d22d3e6746b7cd0aa02c4f03

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-04-22 13:34:37 +0000

      Commit message:


	  
		
 loaded data with use_data() as .rda
 
    
  
    

      Package: AlphaMissenseR

      Commit: 19f4d609ce1f1c8de834aecb093fb35bcfdaa574

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-04-22 13:19:48 +0000

      Commit message:


	  
		
 info about required columns
 
    
  
    

      Package: AlphaMissenseR

      Commit: d21d3d2402ce8f9f8a3feb4ff8cbc2576426970d

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-04-22 13:18:54 +0000

      Commit message:


	  
		
 added ClinVar table from Cheng Supplement
 
    
  
    

      Package: AlphaMissenseR

      Commit: 0419fcde8f87a85e8eca37bf063f0a11e86db0aa

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-04-22 12:53:40 +0000

      Commit message:


	  
		
 imports for integrate_clinvar.R
added man documentation for integrate_clinvar.R
 
    
  
    

      Package: AlphaMissenseR

      Commit: 432e318148af3b3f0bcded7d523e823e25a88cf3

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-04-22 12:19:38 +0000

      Commit message:


	  
		
 renamed function
 
    
  
    

      Package: AlphaMissenseR

      Commit: d02b2182b564dbe2fd7f3e78565d36a4f00c293e

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-04-19 14:55:56 +0000

      Commit message:


	  
		
 added clinvar plotting function
 
    
  
    

      Package: AlphaMissenseR

      Commit: 06ccb6b115c72ace822b54ee7b1388c3a94a1a93

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2024-04-17 21:22:06 +0000

      Commit message:


	  
		
 added vignette for CV integration
 
    
  
    

      Package: eheat

      Commit: 5c0f6087d796353141a5825583010749de4122ca

      Author:  yun <yunyunpp96@outlook.com> 

      Date: 2024-06-26 02:59:58 +0800

      Commit message:


	  
		
 try to fix Biocondcutor check warning
 
    
  
    

      Package: eheat

      Commit: b64c61d094591724c434373a6e9f2d5dfb0934a0

      Author:  yun <yunyunpp96@outlook.com> 

      Date: 2024-06-26 02:45:13 +0800

      Commit message:


	  
		
 fix Bioconductor check error
 
    
  
    

      Package: eheat

      Commit: 1c71cf856924355630958c74b745575f50e21ba0

      Author:  yun <yunyunpp96@outlook.com> 

      Date: 2024-06-26 02:44:43 +0800

      Commit message:


	  
		
 remove file
 
    
  
    

      Package: eheat

      Commit: a64358824c51120997f1854ab226ed722d33d4bc

      Author:  yun <yunyunpp96@outlook.com> 

      Date: 2024-06-26 02:43:51 +0800

      Commit message:


	  
		
 bump version to 0.99.3
 
    
  
    

      Package: eheat

      Commit: b6d437446fff7ef2a85db3e0fd80e5d66657350b

      Author:  yun <yunyunpp96@outlook.com> 

      Date: 2024-06-26 02:43:28 +0800

      Commit message:


	  
		
 add sessionInfo
 
    
  
    

      Package: eheat

      Commit: c96de6a8ccc0ea33902224a8b7edafa04b0f09fc

      Author:  yun <yunyunpp96@outlook.com> 

      Date: 2024-06-26 02:37:36 +0800

      Commit message:


	  
		
 export eheat_prepare.ggAnno method
 
    
  
    

      Package: eheat

      Commit: 4e250ad17fff410d30a3c805d605fe039acf1496

      Author:  yun <yunyunpp96@outlook.com> 

      Date: 2024-06-26 02:28:37 +0800

      Commit message:


	  
		
 bump version to 0.99.2
 
    
  
    

      Package: eheat

      Commit: 291d2c7e3b7f4d3ecab72710aa0826e8953c25bc

      Author:  yun <yunyunpp96@outlook.com> 

      Date: 2024-06-26 02:27:30 +0800

      Commit message:


	  
		
 fix Bioconductor check error
 
    
  
    

      Package: eheat

      Commit: 87a207e9f056f1b000bac2e2227c2c19ef5131d4

      Author:  yun <yunyunpp96@outlook.com> 

      Date: 2024-06-26 02:11:35 +0800

      Commit message:


	  
		
 add NEWs file
 
    
  
    

      Package: eheat

      Commit: 39b1ec02d5993611b4004ddb81d277984411d225

      Author:  yun <yunyunpp96@outlook.com> 

      Date: 2024-06-26 02:09:19 +0800

      Commit message:


	  
		
 bump version to 0.99.1
 
    
  
    

      Package: eheat

      Commit: eb1db704f961afe8fa8dedf67a856ca39c5d6532

      Author:  yun <yunyunpp96@outlook.com> 

      Date: 2024-06-26 02:08:47 +0800

      Commit message:


	  
		
 remove file
 
    
  
    

      Package: eheat

      Commit: bdfa4bb4f5ffb1e8aa373c5aa636d57665d3a2d3

      Author:  yun <yunyunpp96@outlook.com> 

      Date: 2024-06-26 02:07:00 +0800

      Commit message:


	  
		
 fix Docs
 
    
  
    

      Package: eheat

      Commit: c0d1ac05ca2438b73445c4eeca1553c3336505ac

      Author:  yun <yunyunpp96@outlook.com> 

      Date: 2024-06-26 02:06:55 +0800

      Commit message:


	  
		
 sync with devel
 
    
  
    

      Package: eheat

      Commit: 794cf10390287b267cac43047b9d833574da72a2

      Author:  yun <yunyunpp96@outlook.com> 

      Date: 2024-06-26 01:39:56 +0800

      Commit message:


	  
		
 add `eheat` and `eanno`
 
    
  
    

      Package: Macarron

      Commit: ba27b060ae2b6a2bdf2923e5b28d5a8d2eb9ba29

      Author:  sagun <sagun_90@hotmail.com> 

      Date: 2024-06-25 12:26:47 -0400

      Commit message:


	  
		
 Fixed version number
 
    
  
    

      Package: scBubbletree

      Commit: 32e7a2aacae815d177ec0e5abd6cea48855380fb

      Author:  sktron <simo.kitanovski@uni-due.de> 

      Date: 2024-06-25 18:01:32 +0200

      Commit message:


	  
		
 Merge branch 'devel' of github.com:snaketron/scBubbletree into devel
 
    
  
    

      Package: scBubbletree

      Commit: a87394c63ad16efa18bcbfd2480e5619287595b6

      Author:  sktron <simo.kitanovski@uni-due.de> 

      Date: 2024-06-25 18:00:50 +0200

      Commit message:


	  
		
 bump and defaults added
 
    
  
    

      Package: Macarron

      Commit: da995ef02ce299a2c3b31929f6fc782979076a91

      Author:  sagun <sagun_90@hotmail.com> 

      Date: 2024-06-25 11:54:52 -0400

      Commit message:


	  
		
 Fixed Version number
 
    
  
    

      Package: Macarron

      Commit: b1f08ab8691a8c5707ac38e97af0fefc5d601ad9

      Author:  Amrisha Bhosle <abhosle@broadinstitute.org> 

      Date: 2024-06-10 14:02:08 -0400

      Commit message:


	  
		
 Update to NEWS
 
    
  
    

      Package: Macarron

      Commit: b702575b3892cedb0f5525c04353495255b20ac8

      Author:  Amrisha Bhosle <abhosle@broadinstitute.org> 

      Date: 2024-06-10 13:54:50 -0400

      Commit message:


	  
		
 Fixed CITATION
 
    
  
    

      Package: Macarron

      Commit: e035000f6c1d2cee56326fa0fa639ccaf1c4787d

      Author:  Amrisha Bhosle <abhosle@broadinstitute.org> 

      Date: 2024-06-10 13:51:40 -0400

      Commit message:


	  
		
 Version bump
 
    
  
    

      Package: Macarron

      Commit: 1a3d10ff25d50907b3ff035c6e5d4fe92a25b3ab

      Author:  Amrisha Bhosle <abhosle@broadinstitute.org> 

      Date: 2024-06-10 13:39:22 -0400

      Commit message:


	  
		
 Added citation, updated README, and fixed code errors
 
    
  
    

      Package: Macarron

      Commit: 1ecb10a6644c5e9deffbe51a414b665952bf6b8f

      Author:  sagun <sagun_90@hotmail.com> 

      Date: 2024-03-26 18:54:37 -0400

      Commit message:


	  
		
 new issue template
 
    
  
    

      Package: evaluomeR

      Commit: 51d1a403c5ab9f6f931a9abc73f581b35d9f0ebd

      Author:  neobernad <joseantonio.bernabe1@um.es> 

      Date: 2024-06-25 17:21:53 +0200

      Commit message:


	  
		
 Update and bugfix
 
    
  
    

      Package: velociraptor

      Commit: 1aa2e91dc19c6fa513f1b21993ebdff4a3c3abad

      Author:  Kevin Rue-Albrecht <kevinrue67@gmail.com> 

      Date: 2024-06-18 15:09:00 +0100

      Commit message:


	  
		
 Restore previous scvelo environment for Linux (#74)

* restore scvelo environment from bioc 3.18

* document and version bump 
    
  
    

      Package: omXplore

      Commit: 46321fde8ea59723849a217f441c9d56a61ece00

      Author:  Samuel Wieczorek <samuel.wieczorek@cea.fr> 

      Date: 2024-06-25 14:07:26 +0200

      Commit message:


	  
		
 Update
 
    
  
    

      Package: omXplore

      Commit: 36ad359c57034bda020579002c3863c2b117dfef

      Author:  Samuel Wieczorek <samuel.wieczorek@cea.fr> 

      Date: 2024-06-25 13:58:18 +0200

      Commit message:


	  
		
 Update
 
    
  
    

      Package: PhyloProfile

      Commit: 6413ca542bf5e29d77cd001716ddba2537e7ff09

      Author:  trvinh <trvinh@gmail.com> 

      Date: 2024-06-25 12:45:39 +0200

      Commit message:


	  
		
 fixed bug downloading from cluster tree
 
    
  
    

      Package: GeDi

      Commit: a17c59cdff561fce92288dc9cf1eb97c0d16aa81

      Author:  Annekathrin Silvia Ludt <annekathrin@Annekathrins-MacBook-Pro.local> 

      Date: 2024-06-25 11:01:16 +0200

      Commit message:


	  
		
 Updated package version
 
    
  
    

      Package: GeDi

      Commit: b8cd89ded0a55b6429099c871196ff4c32034bfc

      Author:  Annekathrin Silvia Ludt <annekathrin@Annekathrins-MacBook-Pro.local> 

      Date: 2024-06-25 10:55:35 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/devel' into devel
 
    
  
    

      Package: GeDi

      Commit: 2cf3733b2e9a595426c8c7967f95947dd565d643

      Author:  Annekathrin Silvia Ludt <annekathrin@annekathrinsmbp.speedport.ip> 

      Date: 2024-06-24 19:10:48 +0200

      Commit message:


	  
		
 Fixed mistakes and error documented in the NEWS file
 
    
  
    

      Package: GeDi

      Commit: 7df706744e5430ffc9da0dd73e94d93f70440a0a

      Author:  Annekathrin Silvia Ludt <annekathrin@annekathrinsmbp.speedport.ip> 

      Date: 2024-05-19 16:27:17 +0200

      Commit message:


	  
		
 Fixed some typos
 
    
  
    

      Package: GeDi

      Commit: 7fbfb3309e283dc63f25af0063aa3a359c90ca73

      Author:  AnnekathrinSilvia <33468358+AnnekathrinSilvia@users.noreply.github.com> 

      Date: 2024-04-08 14:15:49 +0200

      Commit message:


	  
		
 Merge pull request #23 from AnnekathrinSilvia/bioc_review

Removed font_awesome dependency in vignette 
    
  
    

      Package: GeDi

      Commit: 9fbd26e5ecad12e1a1f31d65d907b882d56ad904

      Author:  Annekathrin Silvia Ludt <annekathrin@annekathrinsmbp.speedport.ip> 

      Date: 2024-04-08 14:15:20 +0200

      Commit message:


	  
		
 Removed font_awesome dependency in vignette
 
    
  
    

      Package: spillR

      Commit: febec27581ce67470995a9fe6999a9fce3960cd8

      Author:  ChristofSeiler <christof.seiler@gmail.com> 

      Date: 2024-06-25 10:19:43 +0200

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: spillR

      Commit: a45a5798ad3110b3761299a8d5bc4ad2cfc55888

      Author:  ChristofSeiler <christof.seiler@gmail.com> 

      Date: 2024-06-25 10:18:04 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/devel'
 
    
  
    

      Package: spillR

      Commit: 9fd0f00465150d4392562cfae1f0f90295752f23

      Author:  ChristofSeiler <christof.seiler@gmail.com> 

      Date: 2024-06-25 09:31:22 +0200

      Commit message:


	  
		
 updated citation and orcid
 
    
  
    

      Package: cytoviewer

      Commit: 86721b2f872fd8f8c9d44930698b07d495868dbd

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2024-06-25 09:49:21 +0200

      Commit message:


	  
		
 Fixed version change conflict
 
    
  
    

      Package: cytoviewer

      Commit: 78c3ded2d58371d87274c46b8faf30e7ccef1f2a

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2024-01-06 13:38:13 +0100

      Commit message:


	  
		
 update BMC link
 
    
  
    

      Package: cytoviewer

      Commit: e6f161e04f022501491e8a3115677a728e8c70c0

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2024-01-05 14:54:30 +0100

      Commit message:


	  
		
 add test
 
    
  
    

      Package: cytoviewer

      Commit: dab7b7a39fbb4221d90b460db036e55c86d457c8

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2024-01-05 14:15:53 +0100

      Commit message:


	  
		
 added unit test
 
    
  
    

      Package: cytoviewer

      Commit: 5fdefc89d46040636f0b4a3d745db5070e4ee374

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2024-01-05 13:04:04 +0100

      Commit message:


	  
		
 add README figure legend
 
    
  
    

      Package: cytoviewer

      Commit: 6251721ff329acb217609ebc7c23764c4379a63c

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2024-01-05 12:50:01 +0100

      Commit message:


	  
		
 add application overview to README
 
    
  
    

      Package: iSEEtree

      Commit: 4ca123970cb2900d13b810b080712790a3113bdc

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2024-06-23 21:46:42 +0300

      Commit message:


	  
		
 Merge pull request #28 from ElySeraidarian/dataparameters

Add data parameters 
    
  
    

      Package: iSEEtree

      Commit: 23a0c21f4b0eda48b0e54bb37cca67d950edcceb

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2024-06-23 21:32:19 +0300

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: iSEEtree

      Commit: 4b95e544343030ff559348b0faa5177d39b4fffa

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2024-06-19 18:43:11 +0300

      Commit message:


	  
		
 Fix tests
 
    
  
    

      Package: iSEEtree

      Commit: 11033d12455e9fff204df2eb3cd65bd73489bafb

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2024-06-19 18:11:48 +0300

      Commit message:


	  
		
 Make changes to RDAPlot panel
 
    
  
    

      Package: iSEEtree

      Commit: 972a280c3e00c58592dce050328dfe114a6fcfe3

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2024-06-19 17:34:37 +0300

      Commit message:


	  
		
 Play with RowTreePlot visual params
 
    
  
    

      Package: iSEEtree

      Commit: 5dd0c70913baa6c338c6e41e9acbd19dee3ab878

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-19 12:00:52 +0300

      Commit message:


	  
		
 Changes to checkboxes UI RowTreePlot
 
    
  
    

      Package: iSEEtree

      Commit: df5d3312c35e2bdec7ff8b3f9243abb074d30188

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-18 11:42:29 +0300

      Commit message:


	  
		
 Fixed issues for checkboxes
 
    
  
    

      Package: iSEEtree

      Commit: 708bc078230e4a93096b09ca6f76dcb6d2e87945

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-17 11:47:22 +0300

      Commit message:


	  
		
 trying rework visual params RowTreePlot
 
    
  
    

      Package: iSEEtree

      Commit: e855155f6f1466d1155e3fd0aec78a47a293cec5

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-14 15:37:28 +0300

      Commit message:


	  
		
 Fixed tests
 
    
  
    

      Package: iSEEtree

      Commit: d04da50c00dcfd31cd73c4f8523b2d2440d34b23

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-14 15:32:09 +0300

      Commit message:


	  
		
 Fixed RDAPlot parameters unresponsive changes
 
    
  
    

      Package: iSEEtree

      Commit: 76d3c71d6b79dbad2b80f820f50ad452c2650acf

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-14 14:58:17 +0300

      Commit message:


	  
		
 Merge branch 'dataparameters' of github.com:ElySeraidarian/iSEEtree into dataparameters
 
    
  
    

      Package: iSEEtree

      Commit: 08d8378dab484ec792fc671487d63f2b0bbbf8d4

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-14 14:58:00 +0300

      Commit message:


	  
		
 Added import methods
 
    
  
    

      Package: iSEEtree

      Commit: 51766f894f5cbd5d5159f4905ac58c544b421a90

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2024-06-14 14:35:44 +0300

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/dataparameters' into dataparameters
 
    
  
    

      Package: iSEEtree

      Commit: de0ae1f658e0080bdf3bf45867ea702a3689e8ae

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2024-06-14 14:35:27 +0300

      Commit message:


	  
		
 Fix .list_taxa for se with 1 rank
 
    
  
    

      Package: iSEEtree

      Commit: 773aea43dee11e77d3bc42bb339c625021f7c60c

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-14 14:07:37 +0300

      Commit message:


	  
		
 Fixed order_sample_by issue
 
    
  
    

      Package: iSEEtree

      Commit: d7cd325e8436159602d85b8d2497c082f3da756e

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2024-06-14 12:52:14 +0300

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/dataparameters' into dataparameters
 
    
  
    

      Package: iSEEtree

      Commit: 362457a6bd861df9aacc6601a161a551a7417f1e

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2024-06-14 12:50:42 +0300

      Commit message:


	  
		
 Fix sample order issue in plotAbundance panel
 
    
  
    

      Package: iSEEtree

      Commit: 49f8afbf546ce85149d1c19b6f592952e540adb2

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-14 12:30:48 +0300

      Commit message:


	  
		
 Added RowTreePlot visual parameters
 
    
  
    

      Package: iSEEtree

      Commit: 699726cfc893d22ce7fb184a547916e19a328646

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-13 14:43:00 +0300

      Commit message:


	  
		
 Fixed last iSEE::: call
 
    
  
    

      Package: iSEEtree

      Commit: 9a0a7ad2de9b6cb6d430c085e9693402f5c2c6a5

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-13 14:41:23 +0300

      Commit message:


	  
		
 Updated documentation & tests also removed iSEE::: calls
 
    
  
    

      Package: iSEEtree

      Commit: d41c3068433359690cc2f40011890dc4db9e72f0

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-13 14:15:36 +0300

      Commit message:


	  
		
 Added RDAPlot visual parameters with group checkbox
 
    
  
    

      Package: iSEEtree

      Commit: e1e8b680e96db1046bce29fab8c8b994efa87106

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-13 11:08:47 +0300

      Commit message:


	  
		
 Row data order sample by example
 
    
  
    

      Package: iSEEtree

      Commit: a208a07c01e2d2f907f59bdc575523a453ca3771

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-12 13:49:32 +0300

      Commit message:


	  
		
 Added order_sample_by & decreasing as data parameters
 
    
  
    

      Package: iSEEtree

      Commit: cc9706bc746aca80c6e27a04ebb2697fd1972cdb

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-10 15:58:45 +0300

      Commit message:


	  
		
 Switched for checkbox order_descending
 
    
  
    

      Package: iSEEtree

      Commit: 5507200cf24bd3b42c5c0497a9a25fb7eacd6b87

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-07 12:12:40 +0300

      Commit message:


	  
		
 Fixed tests
 
    
  
    

      Package: iSEEtree

      Commit: 78ff55d6f08ed4262f32c716ace9825322d9bdef

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-07 11:25:21 +0300

      Commit message:


	  
		
 Fixed shape_by parameter
 
    
  
    

      Package: iSEEtree

      Commit: 6a3911478cc08dd68ae20720af13c2f7eff7d37c

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-07 11:09:13 +0300

      Commit message:


	  
		
 Fixes labels & sliders
 
    
  
    

      Package: iSEEtree

      Commit: 2bbd7079e29f36adb7c7c714a9034e48e2042093

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-05 20:38:53 +0300

      Commit message:


	  
		
 Changed documentation
 
    
  
    

      Package: iSEEtree

      Commit: 2bed7cfd32e07964038b42f9619755766e8122b8

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-05 20:06:07 +0300

      Commit message:


	  
		
 fixed parentheses missing
 
    
  
    

      Package: iSEEtree

      Commit: 19b0ccf8725a3228c5ca8a48cd435c7d0ec6b366

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-05 20:03:30 +0300

      Commit message:


	  
		
 Fixed removed panel
 
    
  
    

      Package: iSEEtree

      Commit: a88353c8d99e7febbf241611e5a25a8a31af9114

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-05 19:29:41 +0300

      Commit message:


	  
		
 Trying to add condition selectInput
 
    
  
    

      Package: iSEEtree

      Commit: 01d0c6570a13f2ef11feffe540e77c447dd77f7d

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-05 15:25:17 +0300

      Commit message:


	  
		
 Added add.significance & add.expl.var as data parameters
 
    
  
    

      Package: iSEEtree

      Commit: 41b5600b15ca70944d696e8902d650cd45594170

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-05 15:11:20 +0300

      Commit message:


	  
		
 Added sliders (not working as intended)
 
    
  
    

      Package: iSEEtree

      Commit: fb50cad8ca5a744f051b0788be96ce1333b30b1c

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-05 11:31:42 +0300

      Commit message:


	  
		
 Added order_tree as a data parameter
 
    
  
    

      Package: iSEEtree

      Commit: 4d6afba6594be6311a388802fa6479289c170928

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-05 11:19:45 +0300

      Commit message:


	  
		
 Added order_descending as a data parameter
 
    
  
    

      Package: iSEEtree

      Commit: 1e5223a0c10ceb562cf70f040587b2003a8a2707

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-04 15:49:45 +0300

      Commit message:


	  
		
 Added flipped as a data parameter
 
    
  
    

      Package: iSEEtree

      Commit: 5945e310e78e4c7450b538798cdd7e23beec3a9b

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-04 15:32:51 +0300

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/devel' into dataparameters
 
    
  
    

      Package: iSEEtree

      Commit: 91b85de6351edebb7e9dc5cd187eb219ccda29f6

      Author:  seraidarian <ely.seraidarian@ecole.ensicaen.fr> 

      Date: 2024-06-04 15:32:13 +0300

      Commit message:


	  
		
 Added use_relative as a data parameter
 
    
  
    

      Package: gDRutils

      Commit: a926756798e8b782ae7d0b76bf82dcce43333428

      Author:  darsoo <daro.scig@gmail.com> 

      Date: 2024-06-25 01:48:06 +0200

      Commit message:


	  
		
 Merge pull request #120 from gdrplatform/darsoo-patch-1

Darsoo patch 1 
    
  
    

      Package: gDRutils

      Commit: c9135492c24b6c112ffc67714efc5a92a7a3b823

      Author:  darsoo <daro.scig@gmail.com> 

      Date: 2024-06-25 00:50:29 +0200

      Commit message:


	  
		
 Update NEWS.md 
    
  
    

      Package: gDRutils

      Commit: b3888421ea3ed1cef9c15e6d706268b857dce86a

      Author:  darsoo <daro.scig@gmail.com> 

      Date: 2024-06-24 17:52:15 +0200

      Commit message:


	  
		
 Update NEWS.md 
    
  
    

      Package: gDRutils

      Commit: c659d580261716c7aa7481e14deccb8c636831a4

      Author:  darsoo <daro.scig@gmail.com> 

      Date: 2024-06-24 17:49:20 +0200

      Commit message:


	  
		
 Update DESCRIPTION 
    
  
    

      Package: gDRutils

      Commit: 1612ede58f4a8ff5e45e924315e6e08247a9bc4b

      Author:  darsoo <daro.scig@gmail.com> 

      Date: 2024-06-24 17:47:32 +0200

      Commit message:


	  
		
 Added  purl = FALSE for error in vignette to prevent error in check 
    
  
    

      Package: Cepo

      Commit: 48144fb8f94c1ea5afaa8c707e9fbefe3ded3d7b

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2024-06-25 05:00:36 +1000

      Commit message:


	  
		
 update pkgdown yaml
 
    
  
    

      Package: Cepo

      Commit: 6e5d4c09f9e68ced63cfbd0b90b36e5a7e5962d9

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2024-06-25 04:34:33 +1000

      Commit message:


	  
		
 remove oldrel-1 from bioc check
 
    
  
    

      Package: Cepo

      Commit: 2995a78c8d8d0b6acb3af0426e9b0dd1a74c6d7f

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2024-06-25 04:30:17 +1000

      Commit message:


	  
		
 bioc check
 
    
  
    

      Package: Cepo

      Commit: 0ad00751e7e7353465296ea23520531fa5ba7144

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2024-06-25 00:49:14 +1000

      Commit message:


	  
		
 bioc check
 
    
  
    

      Package: Cepo

      Commit: 8b0f3b081ef2d2ad18a007c5be15947d7e48e53a

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2024-06-25 00:00:46 +1000

      Commit message:


	  
		
 bioc check
 
    
  
    

      Package: Cepo

      Commit: 5b3ae841506e00a18119c6dd17588979ec923e2a

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2024-06-24 23:47:43 +1000

      Commit message:


	  
		
 bioc check
 
    
  
    

      Package: Cepo

      Commit: 34f67076d1fe7a1b333c1711b24e907c961e7949

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2024-06-24 22:57:47 +1000

      Commit message:


	  
		
 fix magick bug
 
    
  
    

      Package: Cepo

      Commit: 86ba1b968914097d6347d4af8d145a88c51b1d17

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2024-06-24 21:38:51 +1000

      Commit message:


	  
		
 update gha version
 
    
  
    

      Package: Cepo

      Commit: fc11bc304e602ee2a7b1c1b76fe92417b9b1a6c5

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2024-06-24 21:32:03 +1000

      Commit message:


	  
		
 update gha version
 
    
  
    

      Package: adverSCarial

      Commit: d84ab6665d276c26bb6551dc4a2ff8838b28d284

      Author:  GhislainFievet <ghislain.fievet@gmail.com> 

      Date: 2024-06-24 16:18:48 +0200

      Commit message:


	  
		
 vign01 IGD4C example
 
    
  
    

      Package: ginmappeR

      Commit: 40d62d88763cdba0ee013e473dd4ab78cc4a22fe

      Author:  fsola <fsola@us.es> 

      Date: 2024-06-24 15:41:52 +0200

      Commit message:


	  
		
 Release 1.1.2
 
    
  
    

      Package: ginmappeR

      Commit: 081ec3e0357320c8828f2c29e85127db4365855a

      Author:  fsola <fsola@us.es> 

      Date: 2024-06-24 15:41:07 +0200

      Commit message:


	  
		
 Release 1.0.2
 
    
  
    

      Package: PhyloProfile

      Commit: 52b660c75d9ee73eba3519d62b15d1c547c7ef09

      Author:  trvinh <trvinh@gmail.com> 

      Date: 2024-06-24 14:36:47 +0200

      Commit message:


	  
		
 option to sort genes by defined list
 
    
  
    

      Package: Cepo

      Commit: a38b8052ea157cdbb306545713c1da302c028fe8

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2024-06-24 20:32:14 +1000

      Commit message:


	  
		
 bioc check
 
    
  
    

      Package: Cepo

      Commit: 9366bcd232c262f355b0378cd9c77f60ce142718

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2024-06-24 20:16:21 +1000

      Commit message:


	  
		
 bioc check
 
    
  
    

      Package: Cepo

      Commit: bfb2de7348e087d8d8133e7ffe0b01b9c40b01c7

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2024-06-24 19:34:27 +1000

      Commit message:


	  
		
 bioc check
 
    
  
    

      Package: pgxRpi

      Commit: 8dbc10f307ad4b6a74829dfb79f23e2bace8cfeb

      Author:  hangjiaz <zhaohj314@gmail.com> 

      Date: 2024-06-24 12:04:42 +0200

      Commit message:


	  
		
 version bump in devel
 
    
  
    

      Package: pgxRpi

      Commit: 0e7db5f99fd9ea040c140a0cc8f2460608e16535

      Author:  hangjiaz <zhaohj314@gmail.com> 

      Date: 2024-06-24 12:03:48 +0200

      Commit message:


	  
		
 adapt for dorpping survival info in biosamples
 
    
  
    

      Package: biomaRt

      Commit: ddf78e12b8614205251e37cb2c7b24d9f3908b85

      Author:  Mike Smith <grimbough@gmail.com> 

      Date: 2024-06-24 11:22:38 +0200

      Commit message:


	  
		
 Update NEWS
 
    
  
    

      Package: biomaRt

      Commit: 6e73bb6e4f366d27f41c8cd842b45b1ea2eeb612

      Author:  Mike Smith <grimbough@gmail.com> 

      Date: 2024-06-24 11:08:09 +0200

      Commit message:


	  
		
 Remove weird vignette stuff
 
    
  
    

      Package: biomaRt

      Commit: 375192afca65d644a9683f7097f73d2499bb2e56

      Author:  Mike Smith <grimbough@gmail.com> 

      Date: 2024-06-24 11:07:55 +0200

      Commit message:


	  
		
 Don't drop dimensions - fixes issue with wormbase mart
 
    
  
    

      Package: MatrixQCvis

      Commit: 0387b32725b56c1bb68f3f60ff414ee5e3bc99a2

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-24 11:23:05 +0200

      Commit message:


	  
		
 bump to version 1.13.4
 
    
  
    

      Package: MatrixQCvis

      Commit: 47dec451b58a21391c12ed1fea8183f2c83e2dab

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-24 11:02:43 +0200

      Commit message:


	  
		
 update vignette, mention ComBat as batch correction method
 
    
  
    

      Package: biomaRt

      Commit: cad6a3e154dc8f9432bcead7cb435cd65c9bcb9b

      Author:  Mike Smith <grimbough@gmail.com> 

      Date: 2024-06-24 10:47:16 +0200

      Commit message:


	  
		
 Update actions workflow to newer runners
 
    
  
    

      Package: biomaRt

      Commit: 011e9e222250b20851dfcff760659067523243a2

      Author:  Mike Smith <grimbough@gmail.com> 

      Date: 2024-06-24 10:41:31 +0200

      Commit message:


	  
		
 Typo
 
    
  
    

      Package: biomaRt

      Commit: de84f20b2728a14eea24c0c4c1a1d0a92b45948f

      Author:  Mike Smith <grimbough@gmail.com> 

      Date: 2024-06-24 10:23:07 +0200

      Commit message:


	  
		
 Update news
 
    
  
    

      Package: biomaRt

      Commit: bbbab5cbd4a057c7bebae574398c32943806dfe2

      Author:  Mike Smith <grimbough@gmail.com> 

      Date: 2024-06-24 10:21:07 +0200

      Commit message:


	  
		
 Remove deprecated argument from man page
 
    
  
    

      Package: biomaRt

      Commit: c27c7a9482a47fdc5f8368fad1d8cfa3b8f3891f

      Author:  Mike Smith <grimbough@gmail.com> 

      Date: 2024-06-24 10:20:37 +0200

      Commit message:


	  
		
 Version bump
 
    
  
    

      Package: biomaRt

      Commit: 259cdace6c4ce3693b17f30b4854355a41004aa8

      Author:  Mike Smith <grimbough@gmail.com> 

      Date: 2024-06-24 10:16:34 +0200

      Commit message:


	  
		
 Try reading filters table with different encoding if utf-8 fails
 
    
  
    

      Package: biomaRt

      Commit: 413485c86924f6cfde1390948678fd08ea2bb9a8

      Author:  Mike Smith <grimbough@gmail.com> 

      Date: 2024-06-24 10:14:15 +0200

      Commit message:


	  
		
 Remove some defunct and deprecated functions
 
    
  
    

      Package: Cepo

      Commit: fe5e838a5e9cfcf78e673cd45f16988bcbe74c87

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2024-06-24 18:15:18 +1000

      Commit message:


	  
		
 bioc friendly gha
 
    
  
    

      Package: Cepo

      Commit: 99426e39403c6d63835eade26ef8c9ee3b0e1565

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2024-06-24 15:09:30 +1000

      Commit message:


	  
		
 package bump
 
    
  
    

      Package: Cepo

      Commit: 44c7269a10f8186f71610f9a1a6d003f0e2cb345

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2024-06-24 15:07:05 +1000

      Commit message:


	  
		
 fix getGeneSets bug
 
    
  
    

      Package: Cepo

      Commit: c5d6f1c928efd76e8c1b8f10e97e49233d11c4a1

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2024-06-24 14:20:57 +1000

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/master'
 
    
  
    

      Package: Cepo

      Commit: 1ef0e978159a06dbb377b4c6fb4c5789f1536140

      Author:  CSB Yang Laboratory <10148940+PYangLab@users.noreply.github.com> 

      Date: 2023-03-01 13:27:58 +1100

      Commit message:


	  
		
 Update README.md 
    
  
    

      Package: Cepo

      Commit: b18ffdb5bf2f0bd97fa3122e728dc2ba5f48ffa3

      Author:  CSB Yang Laboratory <10148940+PYangLab@users.noreply.github.com> 

      Date: 2023-03-01 13:27:25 +1100

      Commit message:


	  
		
 Update README.md 
    
  
    

      Package: Cepo

      Commit: 74e8a2222d5c5fac13dac378249e1cc7351a1d64

      Author:  Hani Jieun Kim <hani.kim127@gmail.com> 

      Date: 2022-08-16 08:30:46 +1000

      Commit message:


	  
		
 Update exprsPct = 0.05 as default argument
 
    
  
    

      Package: standR

      Commit: 7d8b9f469b854c6b34a87410736c4abc255db69b

      Author:  ningbioinfo <ning.liu@adelaide.edu.au> 

      Date: 2024-06-24 12:56:01 +0930

      Commit message:


	  
		
 update: fix a bug when finding NCG, added a buffer to avoid log0.
 
    
  
    

      Package: systemPipeR

      Commit: e6b45eaa7052fa4f64e5fdb2bb5af05c4a0c1885

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2024-06-23 18:11:08 -0700

      Commit message:


	  
		
 vignette updates
 
    
  
    

      Package: hoodscanR

      Commit: d82f1d24b544a774395dc910a3c7acdc841a8c32

      Author:  ningbioinfo <ning.liu@adelaide.edu.au> 

      Date: 2024-06-24 10:09:04 +0930

      Commit message:


	  
		
 add a function to make sure spatialCoords have rownames
 
    
  
    

      Package: scDiagnostics

      Commit: 516db8afee63ef5a91fabf4e22dc7987d2626bc0

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-23 15:48:23 -0400

      Commit message:


	  
		
 Trigger build.
 
    
  
    

      Package: scDiagnostics

      Commit: 87e16b66be15c78ae32a396466fb17afcb127457

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-23 15:47:21 -0400

      Commit message:


	  
		
 Merge pull request #55 from AnthonyChristidis/main

Modify vignette for size. 
    
  
    

      Package: scDiagnostics

      Commit: a9227781e27b1974e4d8e185c667f78a7377808a

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-23 15:46:59 -0400

      Commit message:


	  
		
 Modify vignette for size.
 
    
  
    

      Package: scDiagnostics

      Commit: 08f7f24edabb75e845ed77bf9d04b960a5b0d1e9

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-23 15:27:15 -0400

      Commit message:


	  
		
 Merge pull request #15 from ccb-hms/main

PR from ccb-hms. 
    
  
    

      Package: scDiagnostics

      Commit: 5280d5240b366d6a5174f506e951cd7c0200c3d9

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-23 15:18:19 -0400

      Commit message:


	  
		
 Trigger Bioconductor build.
 
    
  
    

      Package: scDiagnostics

      Commit: 3b75ef0c4feae28061efd1147a4ab1477691e4b9

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-23 14:37:46 -0400

      Commit message:


	  
		
 Merge pull request #54 from AnthonyChristidis/main

Merge pull request #14 from ccb-hms/main 
    
  
    

      Package: scDiagnostics

      Commit: dc4b155fb5ac63b28a591ac880ecee0105a46a68

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-23 14:37:17 -0400

      Commit message:


	  
		
 Merge pull request #14 from ccb-hms/main

Merge pull request #53 from AnthonyChristidis/main 
    
  
    

      Package: scDiagnostics

      Commit: 50264cef3a0c5ecb0d91ecb2cbd30806ef1c5448

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-23 14:36:52 -0400

      Commit message:


	  
		
 Merge pull request #53 from AnthonyChristidis/main

Temporarily reduce size of vignette. 
    
  
    

      Package: scDiagnostics

      Commit: ce5c1ea75cebc368ea27ad3030f3ec59fc85e5fa

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-23 14:35:45 -0400

      Commit message:


	  
		
 Temporarily reduce size of vignette.
 
    
  
    

      Package: scDiagnostics

      Commit: 3346d67ba31b2bcfd7b45e46c5af6cbb8ca063c3

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-22 23:03:17 -0400

      Commit message:


	  
		
 Merge pull request #13 from ccb-hms/main

PR from ccb-hms version. 
    
  
    

      Package: Pigengene

      Commit: e04cac6c9f4b7c19ba4c47a4d3c4608b5e637a83

      Author:  Habil Zare <zare@uthscsa.edu> 

      Date: 2024-06-23 11:56:04 -0500

      Commit message:


	  
		
 Habil: V 1.31.2, doMinimize
 
    
  
    

      Package: COTAN

      Commit: 2af29e327fa637bd44342429415020e30bed215f

      Author:  Marco Fantozzi <57561972+trinetra75@users.noreply.github.com> 

      Date: 2024-06-23 15:59:49 +0200

      Commit message:


	  
		
 No saving of Seurat objects in `cellsUniformClustering()` (#79)

Even in the cases when the `saveObj` parameter is set to `TRUE`

Co-authored-by: Silvia Giulia Galfre <49807846+seriph78@users.noreply.github.com> 
    
  
    

      Package: COTAN

      Commit: 55dc15dc488d3965379cd76a252fe99caad6f593

      Author:  Marco Fantozzi <57561972+trinetra75@users.noreply.github.com> 

      Date: 2024-06-23 15:52:12 +0200

      Commit message:


	  
		
 Splitted data normalization getter (#78)

* Splitted function `getNormalizedData()` in two

Deprecated the function `getNormalizedData()`
In its place there are now: `getNuNormData()` and
`getLogNormData()`

* Fixed small bug

---------

Co-authored-by: Silvia Giulia Galfre <49807846+seriph78@users.noreply.github.com> 
    
  
    

      Package: COTAN

      Commit: d349d1fe126a981091dc7c1f59964de5c034a8a4

      Author:  Marco Fantozzi <57561972+trinetra75@users.noreply.github.com> 

      Date: 2024-06-23 15:34:23 +0200

      Commit message:


	  
		
 Improved merge with multi-step thresholds (#77)

* Rewritten `mergeUniformCellsClusters()`

Now the function tests all possible pair merges in each batch and
thus merge the pairs with a lower fraction of genes above the threshold

It can also re-use previous runs checks, even in cases when the thrshold
has been changed

* First round of bug-fixes

Cleaned up `mergeClusters()` code

* Fixed minor issues and documentation

Final spet of stage 1: merge with single threshold!

* Now merge uses multiple steps at different GDI thresholds

The function `mergeUniformCellsClusters()` now checks for merge at different
GDI thresholds in steps from the very strict 1.37 up to given one.
This ensures that most suitable pairs are merged first.
The code re-uses the results of checks done with the previous thresholds

* Fixed issues with batch_size in the merge

Now it will loop twice at the beginning before any merge 
    
  
    

      Package: COTAN

      Commit: 1b90905b01724196b031059d9117db4e1735a998

      Author:  Marco Fantozzi <57561972+trinetra75@users.noreply.github.com> 

      Date: 2024-06-19 09:30:34 +0200

      Commit message:


	  
		
 Bugfix/plot functions issues (#76)

* Fixed minor issues with functions: `GDIPlot()` and `clustersMarkersHeatmapPlot()`

Now parameter `groupMarkers` is optional.

* Bumped-up version and updated NEWS.md 
    
  
    

      Package: sesame

      Commit: 18d86699c82230d2dc4bc5612098d7d6f45f1c9b

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2024-06-23 09:10:23 -0400

      Commit message:


	  
		
 added back attachManifest, bump to 1.23.7
 
    
  
    

      Package: scDiagnostics

      Commit: 81ce49044abd984190b8eb5381e3734f3fff55e1

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-22 23:00:38 -0400

      Commit message:


	  
		
 Completed merge with origin/main
 
    
  
    

      Package: scDiagnostics

      Commit: 804f9b722baff6591f0915787fb7b12db028ffcd

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-22 22:50:58 -0400

      Commit message:


	  
		
 Update DESCRIPTION file to trigger build.
 
    
  
    

      Package: scDiagnostics

      Commit: 859cb99003aca1867515658f7a76da46292a0659

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-22 22:50:20 -0400

      Commit message:


	  
		
 Merge pull request #52 from AnthonyChristidis/main

Update format of README file. 
    
  
    

      Package: scDiagnostics

      Commit: 66435ffe35829c5e06f06490e5b5fe1cf916e360

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-22 22:49:56 -0400

      Commit message:


	  
		
 Update format of README file.
 
    
  
    

      Package: scDiagnostics

      Commit: a05bbd924e285996f6caec7227e9dd1199304d80

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-22 22:20:25 -0400

      Commit message:


	  
		
 Merge pull request #12 from ccb-hms/main

Update DESCRIPTION to trigger build. 
    
  
    

      Package: scDiagnostics

      Commit: 1b7a28156b21942a5c4052a2c5bb74414f1d3780

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-22 22:18:23 -0400

      Commit message:


	  
		
 Merge pull request #11 from ccb-hms/main

Merge pull request #51 from AnthonyChristidis/main 
    
  
    

      Package: scDiagnostics

      Commit: e4ddfd6b9de05731c56f89479292851fbbabd45d

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-22 22:19:39 -0400

      Commit message:


	  
		
 Update DESCRIPTION to trigger build.
 
    
  
    

      Package: scDiagnostics

      Commit: 3c9108ad007f32c42f28b8898972a83db6d4d866

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-22 21:33:06 -0400

      Commit message:


	  
		
 Merge pull request #51 from AnthonyChristidis/main

Temporarily reduce size of vignette. 
    
  
    

      Package: scDiagnostics

      Commit: 7adc967aa5e78e06abab286dd1f2ec11c44483ba

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-22 20:54:11 -0400

      Commit message:


	  
		
 Merge pull request #10 from ccb-hms/main

Update DESCRIPTION to trigger build. 
    
  
    

      Package: scDiagnostics

      Commit: b1af8824cce261b8a04db566065ddee206251894

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-22 20:53:32 -0400

      Commit message:


	  
		
 Temporarily reduce size of vignette.
 
    
  
    

      Package: scDiagnostics

      Commit: 1694e0118494405b037f3fa58457db6772289666

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-22 19:41:54 -0400

      Commit message:


	  
		
 Merge pull request #9 from ccb-hms/main

PR from ccb-hms version. 
    
  
    

      Package: systemPipeR

      Commit: 55ea802954ee1d3f715d5facfc8d2195070b6a75

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2024-06-22 18:41:28 -0700

      Commit message:


	  
		
 vignette edits
 
    
  
    

      Package: scDiagnostics

      Commit: 2455219c38148c30adae28bdf11ab2982d08a5b4

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-22 19:59:45 -0400

      Commit message:


	  
		
 Update DESCRIPTION to trigger build.
 
    
  
    

      Package: scDiagnostics

      Commit: c812f48e7a068bfc6d0ac6653578cf18d4d7d4ff

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-22 19:35:13 -0400

      Commit message:


	  
		
 Update DESCRIPTION file to trigger new build.
 
    
  
    

      Package: scDiagnostics

      Commit: 641ab1f4bb9cb037d941f3653594ba7fbd2eb5cc

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-22 19:08:41 -0400

      Commit message:


	  
		
 Merge pull request #50 from AnthonyChristidis/main

Fix errors in plot functions. Also update DESCRIPTION file. 
    
  
    

      Package: scDiagnostics

      Commit: 28debf98bc1925e6a8ec27f7b3695c498cc72a5f

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-22 18:16:36 -0400

      Commit message:


	  
		
 Merge pull request #8 from ccb-hms/main

Merge pull request #49 from AnthonyChristidis/main 
    
  
    

      Package: scDiagnostics

      Commit: c243e9cd736dfb9d1461e974c6c400d0c86489ae

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-22 16:40:45 -0400

      Commit message:


	  
		
 Add ORCID to DESCRIPTION file.
 
    
  
    

      Package: scDiagnostics

      Commit: c65299a7ab68d700f268d19322d642b022a792d0

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-22 16:40:27 -0400

      Commit message:


	  
		
 Fix error in plot function of comparePCASubspace, and update appearance of plots to match other functions.
 
    
  
    

      Package: scDiagnostics

      Commit: d1af3634fb498e559a60bd09be483c8c9321f0c8

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-22 13:25:45 -0400

      Commit message:


	  
		
 Merge pull request #49 from AnthonyChristidis/main

Fix errors from Bioconductor submission check. 
    
  
    

      Package: scDiagnostics

      Commit: 5ee7467376367f2e69334aee2475b785183eda63

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-22 01:00:33 -0400

      Commit message:


	  
		
 Update gitignore file to remove Rproj file.
 
    
  
    

      Package: scDiagnostics

      Commit: f881210f3329279e8d9b4d3167d36f65fcb9c631

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-22 00:56:51 -0400

      Commit message:


	  
		
 Merge pull request #7 from ccb-hms/main

PR from ccb-hms version. 
    
  
    

      Package: scDiagnostics

      Commit: c761afb77578387442c39393947c4075497777f4

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-22 00:26:29 -0400

      Commit message:


	  
		
 Update files to ignore.
 
    
  
    

      Package: scDiagnostics

      Commit: b9566d94e03ed8676dba8c6fc3982be7686c14c0

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-22 00:12:36 -0400

      Commit message:


	  
		
 Update file type of NEWS file.
 
    
  
    

      Package: scDiagnostics

      Commit: 39f6ee5fc07506cdf31b1e6e7dd6d9b6afb233a0

      Author:  Anthony Christidis <anthony.christidis@stat.ubc.ca> 

      Date: 2024-06-22 00:10:35 -0400

      Commit message:


	  
		
 Fix minor typos in documentation of functions.
 
    
  
    

      Package: scDiagnostics

      Commit: 9c5cda85202f7f9f39873854b0c5d863b4622223

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-21 22:33:06 -0400

      Commit message:


	  
		
 Delete scDiagnostics.Rproj 
    
  
    

      Package: scDiagnostics

      Commit: 2ec62b82d1a225a3b2153acb76bab2e7927cc1d0

      Author:  Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com> 

      Date: 2024-06-21 22:32:42 -0400

      Commit message:


	  
		
 Delete scDiagnostics.Rproj 
    
  
    

      Package: scBubbletree

      Commit: 1824e0f0b21cd7c86c5bd4b0ef3182486049ad34

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2024-06-22 15:12:13 +0200

      Commit message:


	  
		
 legend title above
 
    
  
    

      Package: scBubbletree

      Commit: e2d7b75118904de31cbd663b5cdd7c042d884b85

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2024-06-22 14:48:56 +0200

      Commit message:


	  
		
 bump v and guides width fix
 
    
  
    

      Package: alabaster.ranges

      Commit: 9483fb6567f7725930676b998cb8652ce8b69c2b

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2024-06-21 12:48:33 -0700

      Commit message:


	  
		
 Simplified the NEWS on the master branch.

Can't be bothered to track changes for individual patch numbers; do that
in the RELEASE_* branches instead.
 
    
  
    

      Package: alabaster.ranges

      Commit: 0baaee8dba1b7785ca29116b8279d12bcc843a24

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2024-06-21 12:44:20 -0700

      Commit message:


	  
		
 Open all HDF5 files in read-only mode for readObject()-dispatched functions.
 
    
  
    

      Package: alabaster.matrix

      Commit: 3d04935f3e76d6a7159ee47b8f79f7f1c21c6cde

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2024-06-21 12:25:51 -0700

      Commit message:


	  
		
 Open HDF5 files in read-only mode for readObject()-dispatched functions.
 
    
  
    

      Package: alabaster.base

      Commit: 02c5473799a5055080cbb29d32eb78ea104df5c2

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2024-06-21 12:24:14 -0700

      Commit message:


	  
		
 Minor fix to the README to avoid being so fine-grained.

Too much of a hassle to keep track of individual patch numbers on the
master branch; handle it on the RELEASE_* branches if it matters.
 
    
  
    

      Package: alabaster.base

      Commit: 2c7235f87a773ecc8457ffcfc10611b60d6af50f

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2024-06-21 12:23:00 -0700

      Commit message:


	  
		
 Open HDF5 files in read-only mode in readObject()-dispatched functions.
 
    
  
    

      Package: ResidualMatrix

      Commit: dd8b863c9132e43450ce687223a25f7fbc066d8f

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2024-06-21 10:27:25 -0700

      Commit message:


	  
		
 Improved the efficiency of the PCA example in the vignette.
 
    
  
    

      Package: scBubbletree

      Commit: 976fe35a46a0b546612df801f1e1f03a2cab3120

      Author:  sktron <simo.kitanovski@uni-due.de> 

      Date: 2024-06-21 18:30:37 +0200

      Commit message:


	  
		
 fix multicore
 
    
  
    

      Package: MatrixQCvis

      Commit: a72584915e15955fb5596f8f45ea605d1a50ac6a

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-21 17:58:43 +0200

      Commit message:


	  
		
 bump to version 1.13.3
 
    
  
    

      Package: MatrixQCvis

      Commit: 4db6affc7803b1383eeb55f62bac83a5be21df40

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-21 17:47:26 +0200

      Commit message:


	  
		
 change length of keep_rows in batchCorrectionAssay (ComBat)
 
    
  
    

      Package: MatrixQCvis

      Commit: 75205a017acd085396a52960f8d20cda2c46dee8

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-21 16:10:56 +0200

      Commit message:


	  
		
 refine ComBat implementation
 
    
  
    

      Package: MatrixQCvis

      Commit: 5842dd48ee5699504e49202b60fba4ca66c730bf

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-21 16:08:25 +0200

      Commit message:


	  
		
 add limitsize = FALSE to ggsave
 
    
  
    

      Package: MatrixQCvis

      Commit: 968feb47d67ce4bd2c5df7359c0de9e783c1f1b2

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-21 16:08:08 +0200

      Commit message:


	  
		
 add limitsize = FALSE to ggsave
 
    
  
    

      Package: MatrixQCvis

      Commit: 50980a10b42993022dc19bfa775e076fabf3347a

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-21 16:07:48 +0200

      Commit message:


	  
		
 Update module_measuredValues_missingValues.R
 
    
  
    

      Package: MatrixQCvis

      Commit: a2e25aee1e441e6d44837e093bdbb29deaa61934

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-21 16:07:36 +0200

      Commit message:


	  
		
 Update module_de.R
 
    
  
    

      Package: MatrixQCvis

      Commit: 715c2d015b95594cbbe87020046229b52b651a38

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-21 16:07:17 +0200

      Commit message:


	  
		
 Update batchCorrectionAssay.Rd
 
    
  
    

      Package: MatrixQCvis

      Commit: 7ac96f468e48596a96a29bc29aa9e778bf4ec656

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-21 14:59:16 +0200

      Commit message:


	  
		
 remove loading tag when shiny-busy is true
 
    
  
    

      Package: MatrixQCvis

      Commit: d1dce4e6745dfe316b9c66b34c939d648a684cd8

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-20 13:15:57 +0200

      Commit message:


	  
		
 Update module_values.R
 
    
  
    

      Package: MatrixQCvis

      Commit: bfc21cc2a41f107b718c38634b90588fd48d2ded

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-19 17:38:06 +0200

      Commit message:


	  
		
 Update shinyQC.R
 
    
  
    

      Package: MatrixQCvis

      Commit: d5010d92b65a03e0e84c4029b25693dce2e7972c

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-18 12:57:47 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: 305b409b67d406eaba254562bcc08396a9f0e343

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-18 11:34:09 +0200

      Commit message:


	  
		
 remove manual installation
 
    
  
    

      Package: MatrixQCvis

      Commit: d23012301838cd00e19fbf62e7eed954ae72f6cf

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-18 11:33:31 +0200

      Commit message:


	  
		
 replace " " by tab in DESCRIPTION
 
    
  
    

      Package: MatrixQCvis

      Commit: bfb2b88690c9f971f769507c76dffb5d6be62797

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-18 11:31:36 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: b62aa5b486d2f6c5b22bd5640a32b5185622547c

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-18 11:30:00 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: b305548bf854970bac505738d576fcf4860ff28a

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-18 11:23:26 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: 99bff14edd0177f75bb7734515a5c2d2b7f4ed70

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-18 11:17:05 +0200

      Commit message:


	  
		
 Update DESCRIPTION
 
    
  
    

      Package: MatrixQCvis

      Commit: fb87f20cbefef5dbe6e6f3dcabc066626c3c392d

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-18 11:11:19 +0200

      Commit message:


	  
		
 add sva in imports in DESCRIPTION
 
    
  
    

      Package: MatrixQCvis

      Commit: 7cb716db1af699a373d73bc4947bec339dcc5dc5

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-18 11:08:14 +0200

      Commit message:


	  
		
 add sva::ComBat as batch correction method
 
    
  
    

      Package: MatrixQCvis

      Commit: 9d6453d1aa34eb1846c47d5bfd43431ed2700032

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-12 11:05:02 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: 6773e2e7de55c571affd928db578960a4de0b8f6

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-12 10:58:13 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: a1d21153d98ec76b60fc4b5d07b72fe91eb8bef3

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-12 10:55:30 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: 82566055f27a11f21ba6ddef40c1c50eddd1740e

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-12 10:25:32 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: d68cf1cf7a0b13a0cbee1b3bf5a6c9e7d621d9de

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-12 09:33:49 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: 1fd1c32557f723045827fde0643cae290255f357

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-12 09:30:54 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: df74b2ba7c6cb3e059af25ee8bb9bea1145008fb

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-12 09:22:11 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: a78b659c42c96de1ba606e60a418e75c99cd35e5

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-12 09:12:57 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: d6a368f8903ed15a3fe9916dade29822f5d4e18d

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-12 08:57:03 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: 7ef605fe6ffe0e6c27c1cfd982ad8f76f808f1b8

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-12 08:46:08 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: 71732368189a7cad4f9a0b41b3c5d062d6190d7c

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-11 18:20:03 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: 4b7f0ab0d1e29c5bdf9b4430f983a8fc1374f89a

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-11 17:33:14 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: ae9e7159835d8fb558f137ad8a716de5d627a819

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-11 17:06:48 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: bf404fae5b984bdea120d76c259f29acb94ac81d

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-11 16:44:16 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: 471ae78a59be284e1632cacf1b21753c873293f2

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-11 16:43:47 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: cb48e52a0e8aea693d6af56e8c57c21f4a3d7dbe

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-11 16:30:55 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: bd48a238c6656c231d46f1c521c660f33b01e7c3

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-11 16:29:02 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MatrixQCvis

      Commit: 292d33039b3136734806fbb8cfbea0c1be4128ff

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2024-06-11 16:27:41 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: scBubbletree

      Commit: 79f9a25431c8d2d00ef1705c0c098b9d275993b3

      Author:  sktron <simo.kitanovski@uni-due.de> 

      Date: 2024-06-21 17:15:39 +0200

      Commit message:


	  
		
 commit parallel updates
 
    
  
    

      Package: evaluomeR

      Commit: f422361a2d904a58471c907c8d126810799348b7

      Author:  neobernad <joseantonio.bernabe1@um.es> 

      Date: 2024-06-21 15:42:29 +0200

      Commit message:


	  
		
 BugFix
 
    
  
    

      Package: scater

      Commit: 317a43b14e97eaaeedb97f50ccbd75bf55c37665

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2024-06-21 13:36:00 +0100

      Commit message:


	  
		
 Resolve #209
 
    
  
    

      Package: PolySTest

      Commit: 01d75b45a32aa582b3c5466bdde435b682fa93eb

      Author:  veitveit <veits@bmb.sdu.dk> 

      Date: 2024-06-21 12:49:13 +0200

      Commit message:


	  
		
 inifity to NA
 
    
  
    

      Package: PolySTest

      Commit: 009eef821bf53d2da3d364e5d7a4a4d8cb1a13a5

      Author:  veitveit <veits@bmb.sdu.dk> 

      Date: 2024-06-21 12:29:29 +0200

      Commit message:


	  
		
 rerun limma test
 
    
  
    

      Package: DepecheR

      Commit: 2298002365c1521ef69976e8e90fd8f2a2659906

      Author:  Jakob Theorell <jakob.theorell@ki.se> 

      Date: 2024-06-21 10:54:47 +0100

      Commit message:


	  
		
 Minor bug fixes.
 
    
  
    

      Package: PolySTest

      Commit: 024dad9649719ea2423728d96c9de06562973c62

      Author:  veitveit <veits@bmb.sdu.dk> 

      Date: 2024-06-21 11:08:23 +0200

      Commit message:


	  
		
 updates for bioconductor submission
 
    
  
    

      Package: zellkonverter

      Commit: 328e7ea895196dbac6229ad3076e9b6ed00b7afe

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2024-06-21 10:56:07 +0200

      Commit message:


	  
		
 Merge branch 'RELEASE_3_19' into devel

* RELEASE_3_19:
  Bump release version
  Add example H5AD test
  Fix URL for GTEx 8 tissues dataset in long tests
  Disable anndata v0.7.6 tests on Apple Silicon
 
    
  
    

      Package: zellkonverter

      Commit: c90c58a4880a9f8b093c9fd7cd4fb3a39a51be8f

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2024-06-21 10:52:52 +0200

      Commit message:


	  
		
 Bump release version
 
    
  
    

      Package: zellkonverter

      Commit: 7e14d4c94f9bda9dd07b440981fea094377b2b44

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2024-06-21 10:42:21 +0200

      Commit message:


	  
		
 Add example H5AD test
 
    
  
    

      Package: zellkonverter

      Commit: 48ec4d09c0f18305aaa344ad88f725a00038b50f

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2024-05-27 11:41:29 +0200

      Commit message:


	  
		
 Fix URL for GTEx 8 tissues dataset in long tests
 
    
  
    

      Package: zellkonverter

      Commit: 2319033a4aa2127d74146f78acbeaf3e50759fea

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2024-05-27 11:26:12 +0200

      Commit message:


	  
		
 Disable anndata v0.7.6 tests on Apple Silicon

Python 3.7 is not available via conda here
 
    
  
    

      Package: gemma.R

      Commit: 610f89799bdb202ea3001bd4bda98e1596777fa4

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2024-06-20 20:23:58 -0700

      Commit message:


	  
		
 minor
 
    
  
    

      Package: DMRcate

      Commit: 8f5a45dc3c77716fe53ded757edfa7fa80ab6617

      Author:  timpet <t.peters@garvan.org.au> 

      Date: 2024-06-21 13:55:15 +1000

      Commit message:


	  
		
 DMRcate_3.1.3
 
    
  
    

      Package: gemma.R

      Commit: 4032962df43e8f28f005e94691841a029208f348

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2024-06-20 20:15:51 -0700

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: gemma.R

      Commit: 4790cbcbe4ee17151f3630ac035a14b1b7286a20

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2024-06-20 20:15:04 -0700

      Commit message:


	  
		
 you don't belong here...
 
    
  
    

      Package: gemma.R

      Commit: 86f6f680c148641d408b8bda19310e0feda3bb55

      Author:  ogan Mancarci <ogan.mancarci@gmail.com> 

      Date: 2024-06-19 05:04:29 -0700

      Commit message:


	  
		
 fix option after test
 
    
  
    

      Package: gemma.R

      Commit: bd1e0f495944ae66f1ba28d9964753028d3ebf25

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2024-06-18 20:35:12 -0700

      Commit message:


	  
		
 typo
 
    
  
    

      Package: gemma.R

      Commit: a6e6280e9d5c59469f2dfe3c6c2f034f5a475748

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2024-06-18 20:32:46 -0700

      Commit message:


	  
		
 silence note
 
    
  
    

      Package: gemma.R

      Commit: 782c0f649b7ca2ea80c6727e91129dd1d331d57b

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2024-06-18 20:31:46 -0700

      Commit message:


	  
		
 add dependencies
 
    
  
    

      Package: gemma.R

      Commit: cd2b6659201783c5e7f635f3ebd370c44a3468bd

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2024-06-18 20:15:05 -0700

      Commit message:


	  
		
 tests for inpur compression
 
    
  
    

      Package: gemma.R

      Commit: c9cba08114610b6a129d31e73fc1fcc14a4cd7c4

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2024-06-18 20:14:19 -0700

      Commit message:


	  
		
 json bump
 
    
  
    

      Package: gemma.R

      Commit: 5d8f461cbb6b657ed00c1ed9564e30a4c32e8264

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2024-06-18 20:14:09 -0700

      Commit message:


	  
		
 support compressing long URLs
 
    
  
    

      Package: gemma.R

      Commit: 1e781d7a52a6ccb5784d47851b805bc32265e775

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2024-06-18 20:12:37 -0700

      Commit message:


	  
		
 rebuild endpoints, remove unsupported compressions
 
    
  
    

      Package: gemma.R

      Commit: e0a7dc8bbde9dce082e539f48fc22f32dc8a108c

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2024-06-18 18:55:44 -0700

      Commit message:


	  
		
 add compress_arg
 
    
  
    

      Package: gemma.R

      Commit: 873f91457daaeac2b16e1d6fb9de67fea4fc0652

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2024-06-18 18:55:05 -0700

      Commit message:


	  
		
 add compressibles to registry
 
    
  
    

      Package: gemma.R

      Commit: 76f1e9c884137dcef23fb78049ef798917a631bc

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2024-06-18 18:54:52 -0700

      Commit message:


	  
		
 registry cleanup
 
    
  
    

      Package: gemma.R

      Commit: 8b1fbadfe5175d867826d3f5e0be84e50229f500

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2024-06-18 18:51:49 -0700

      Commit message:


	  
		
 support arrays as internal variables, add compressibles as an internal variable, simplify internal variable processing
 
    
  
    

      Package: SparseArray

      Commit: 6e3c2cf0ca7423473d0f04b76f340112ff1300b4

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-06-20 19:38:06 -0700

      Commit message:


	  
		
 SparseArray 1.5.10

Special-case 'lambda=0' in poissonSparseArray() so the empty
SVT_SparseArray object gets returned instantaneously.
 
    
  
    

      Package: systemPipeR

      Commit: b088c51d55e9183fdd03483673e5e6476a850459

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2024-06-20 19:00:57 -0700

      Commit message:


	  
		
 vignette edits
 
    
  
    

      Package: systemPipeR

      Commit: 097b637a99c97f80abc56eac49f6eb37a9ca0556

      Author:  Thomas Girke <tgirke@citrus.ucr.edu> 

      Date: 2024-06-20 16:09:32 -0700

      Commit message:


	  
		
 Merge pull request #83 from lz100/devel

feat: add quick start section in vignette 
    
  
    

      Package: systemPipeR

      Commit: cc16573a50f7cfa371b9f6feb1c8281239d441a6

      Author:  lz <lz@DESKTOP-MP3UQ3S.localdomain> 

      Date: 2024-06-15 18:21:19 -0700

      Commit message:


	  
		
 feat: add quick start section in vignette
 
    
  
  


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