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Release/2.0.0 #138

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e5b1460
bump version and date
samuel-marsh Sep 15, 2023
a30a6f9
reduce minimum seurat to ensure prior compatibility
samuel-marsh Sep 16, 2023
6b8e234
add MAD stats function
samuel-marsh Sep 16, 2023
ae8c71f
add cell complexity by default to median stats
samuel-marsh Sep 16, 2023
2f34847
update dplyr syntax all_of
samuel-marsh Sep 16, 2023
69ecb7e
Update changelog
samuel-marsh Sep 16, 2023
1f5f3be
bump version and date
samuel-marsh Sep 16, 2023
275244c
Update docs
samuel-marsh Sep 16, 2023
b4abb8a
Update docs
samuel-marsh Sep 16, 2023
70a8b62
bump version
samuel-marsh Sep 16, 2023
e1671ea
speed plotting
samuel-marsh Sep 17, 2023
b577e74
speed updates
samuel-marsh Sep 17, 2023
53573d9
fix error
samuel-marsh Sep 17, 2023
4f23ab4
fix again
samuel-marsh Sep 17, 2023
e7b2c7b
fix another speed check
samuel-marsh Sep 17, 2023
ff5c864
whoops
samuel-marsh Sep 17, 2023
555ebb1
whoops #2
samuel-marsh Sep 17, 2023
82a130e
cells fix
samuel-marsh Sep 17, 2023
c62bf35
update changelog
samuel-marsh Sep 17, 2023
013838f
bump version
samuel-marsh Sep 17, 2023
5a22a07
fix color setting in vlnplot when split.by is not null
samuel-marsh Sep 18, 2023
cb3b80a
fix split colors
samuel-marsh Sep 18, 2023
2f6e7b6
update changelog
samuel-marsh Sep 18, 2023
5512c6a
bump version and date
samuel-marsh Sep 18, 2023
3eb24d0
replace colnames with Cells for Seurat objects
samuel-marsh Sep 18, 2023
56b88eb
replace colnames with cells
samuel-marsh Sep 18, 2023
ddadb11
replace colnames with Cells
samuel-marsh Sep 18, 2023
98b1095
update changelog
samuel-marsh Sep 18, 2023
ee94218
bump version
samuel-marsh Sep 18, 2023
e6442b3
fix barcode rank plots
samuel-marsh Sep 20, 2023
2dec3c3
bump version and date
samuel-marsh Sep 20, 2023
a1b48d9
fix error message
samuel-marsh Sep 20, 2023
8a16437
add top % gene function
samuel-marsh Sep 22, 2023
b8ff590
update changelog
samuel-marsh Sep 22, 2023
e8fb77d
update docs
samuel-marsh Sep 22, 2023
5d364ee
update docs
samuel-marsh Sep 22, 2023
78d1b07
bump version and date
samuel-marsh Sep 22, 2023
847e208
fix dimplot plotting multiple group.by variables
samuel-marsh Sep 22, 2023
611650f
update changelog
samuel-marsh Sep 22, 2023
b2df383
bump version and date
samuel-marsh Sep 22, 2023
236282e
add custom features and warning message
samuel-marsh Sep 23, 2023
23f8513
Update docs
samuel-marsh Sep 23, 2023
fd48166
bump version and date
samuel-marsh Sep 23, 2023
a3308dc
update changelog
samuel-marsh Sep 23, 2023
8fafbdb
Fix iterate by sample when not orig.ident
samuel-marsh Sep 23, 2023
b9c1614
bump version
samuel-marsh Sep 23, 2023
40c4831
Add overall QC function
samuel-marsh Sep 24, 2023
44604da
Update docs
samuel-marsh Sep 24, 2023
9cf2663
fix param errors
samuel-marsh Sep 24, 2023
05d217b
Update docs
samuel-marsh Sep 24, 2023
f44f8b7
Update docs
samuel-marsh Sep 24, 2023
566caa0
update changelog
samuel-marsh Sep 24, 2023
301cda5
bump version
samuel-marsh Sep 24, 2023
740854b
fix parameter name errors
samuel-marsh Sep 24, 2023
487bf38
Update docs
samuel-marsh Sep 24, 2023
9727688
Update changelog
samuel-marsh Sep 24, 2023
174b1ec
bump version
samuel-marsh Sep 24, 2023
735b57e
reorg and add MSigDB retrieval
samuel-marsh Sep 28, 2023
a71ff7e
add assay param
samuel-marsh Sep 29, 2023
bb10e9e
update changelog
samuel-marsh Sep 29, 2023
7f87d79
msigdb gene lists
samuel-marsh Sep 29, 2023
5208f23
update docs
samuel-marsh Sep 29, 2023
e47038e
update data
samuel-marsh Sep 29, 2023
b4f1b96
remove gene list
samuel-marsh Sep 29, 2023
88a4ba6
add msigdb list and document
samuel-marsh Sep 29, 2023
5e0b6d2
add new mSigDB internals
samuel-marsh Sep 29, 2023
3c43a22
add assay param
samuel-marsh Sep 29, 2023
b9b47d5
typo
samuel-marsh Sep 29, 2023
c54e723
Add ieg gene list and documentation
samuel-marsh Sep 29, 2023
895f71f
docs
samuel-marsh Sep 29, 2023
7f8bd83
add ieg retrieval function
samuel-marsh Sep 29, 2023
2550908
Add IEG percent function
samuel-marsh Sep 29, 2023
b13d7f1
update overall qc function
samuel-marsh Sep 29, 2023
ef34be4
update docs
samuel-marsh Sep 29, 2023
8071417
update source info
samuel-marsh Sep 29, 2023
3af5016
update changelog
samuel-marsh Sep 29, 2023
9ded861
update docs
samuel-marsh Sep 29, 2023
3bf2fa6
update changelog
samuel-marsh Sep 29, 2023
ac24df3
bump version and date
samuel-marsh Sep 29, 2023
dc26bd8
reorg functions
samuel-marsh Sep 30, 2023
c8173fd
update docs
samuel-marsh Sep 30, 2023
90d9d25
update changelog
samuel-marsh Sep 30, 2023
b5989c4
bump version and date
samuel-marsh Sep 30, 2023
3c1ac62
add cell cycle scoring to cell qc
samuel-marsh Sep 30, 2023
1052652
update docs
samuel-marsh Sep 30, 2023
ede7c20
Update changelog
samuel-marsh Sep 30, 2023
a6aa9dc
bump version
samuel-marsh Sep 30, 2023
174bf94
fix dotplot scCustom bug
samuel-marsh Sep 30, 2023
b7fdbfd
fix dotplot
samuel-marsh Sep 30, 2023
424c687
fix dotplot
samuel-marsh Sep 30, 2023
c6037f0
case check fix
samuel-marsh Sep 30, 2023
c71cf74
Update changelog
samuel-marsh Sep 30, 2023
26c2567
bump version
samuel-marsh Sep 30, 2023
3111208
typo
samuel-marsh Oct 1, 2023
8f75de6
style fix
samuel-marsh Oct 3, 2023
b21ca67
style
samuel-marsh Oct 3, 2023
92d0aca
update palette defaults
samuel-marsh Oct 3, 2023
f11cae9
update docs
samuel-marsh Oct 3, 2023
94a1e45
update changelog
samuel-marsh Oct 3, 2023
f161ae3
bump version and date
samuel-marsh Oct 3, 2023
51215bf
warning message bug
samuel-marsh Oct 3, 2023
46bed91
fix warning error
samuel-marsh Oct 3, 2023
5c03e03
update changelog
samuel-marsh Oct 3, 2023
d78ad8b
bump version
samuel-marsh Oct 3, 2023
b07fabd
style fix
samuel-marsh Oct 3, 2023
a630ced
min scattermore version
samuel-marsh Oct 4, 2023
e04d778
update changelog
samuel-marsh Oct 4, 2023
5d2553c
bump version and date
samuel-marsh Oct 4, 2023
0b192df
set label if label.box TRUE
samuel-marsh Oct 5, 2023
09b2387
add non-default check
samuel-marsh Oct 5, 2023
9208f0c
Update changelog
samuel-marsh Oct 5, 2023
9d56a72
bump version and date
samuel-marsh Oct 5, 2023
507be67
update violin plot
samuel-marsh Oct 5, 2023
fe21e03
update docs
samuel-marsh Oct 5, 2023
787f059
Update changelog
samuel-marsh Oct 5, 2023
975a0b0
update qc plots with boxplot param
samuel-marsh Oct 5, 2023
af7a014
Update docs
samuel-marsh Oct 5, 2023
ae7511a
remove old median plotting
samuel-marsh Oct 5, 2023
1356ae6
update changelog
samuel-marsh Oct 5, 2023
6456ede
bump version
samuel-marsh Oct 5, 2023
7cbb668
edit name
samuel-marsh Oct 24, 2023
25858cb
edit name
samuel-marsh Oct 24, 2023
38c3bdd
add return qc default internal function
samuel-marsh Oct 24, 2023
205ecba
add QC histogram
samuel-marsh Oct 24, 2023
028d7dd
Update docs
samuel-marsh Oct 24, 2023
144818a
update changelog
samuel-marsh Oct 24, 2023
c8beacc
bump version and date
samuel-marsh Oct 24, 2023
5e5a13a
typo
samuel-marsh Oct 25, 2023
66c6e6e
mito ribo bug fix
samuel-marsh Oct 26, 2023
2d77889
mito ribo fix
samuel-marsh Oct 26, 2023
40d4054
update changelog
samuel-marsh Oct 26, 2023
d48b693
bump version and date
samuel-marsh Oct 26, 2023
c9e4849
add boxplot median check
samuel-marsh Oct 26, 2023
f069de1
typo fix
samuel-marsh Oct 26, 2023
f2820e5
move split to plot utilities, internal, renamed
samuel-marsh Oct 26, 2023
84ee514
deprecate warn
samuel-marsh Oct 26, 2023
7152545
remove temp
samuel-marsh Oct 26, 2023
1b7d26b
add deprecate badge
samuel-marsh Oct 26, 2023
dcf1025
get badge to work
samuel-marsh Oct 26, 2023
a328d0c
update docs
samuel-marsh Oct 26, 2023
332f1a3
update docs
samuel-marsh Oct 26, 2023
405e9f8
update docs
samuel-marsh Oct 26, 2023
f55aefc
update example
samuel-marsh Oct 26, 2023
2717a4d
add FeatureScatter_scCustom
samuel-marsh Oct 26, 2023
8f2537b
add new warning
samuel-marsh Oct 26, 2023
d379a86
Update docs
samuel-marsh Oct 26, 2023
cb467a9
Update NAMESPACE
samuel-marsh Oct 26, 2023
8639aa2
update changelog
samuel-marsh Oct 26, 2023
2f1f02e
bump version
samuel-marsh Oct 26, 2023
a68e0ab
replace full tidyverse call to remove suggests
samuel-marsh Oct 27, 2023
0e9b598
Update changelog
samuel-marsh Oct 27, 2023
5e13092
bump version and date
samuel-marsh Oct 27, 2023
6d1ad3d
update palette default to false for ggplot2 colors
samuel-marsh Oct 27, 2023
7ae85b7
Update changelog
samuel-marsh Oct 27, 2023
86d7be8
update docs
samuel-marsh Oct 27, 2023
80efcc6
bump version
samuel-marsh Oct 27, 2023
5350ca7
replace PackageCheck with rlang equivalent
samuel-marsh Oct 27, 2023
b6c194f
Update NAMESPACE
samuel-marsh Oct 27, 2023
8d58a9a
update changelog
samuel-marsh Oct 27, 2023
268c39a
bump version
samuel-marsh Oct 27, 2023
d2d01f4
isTRUE
samuel-marsh Oct 27, 2023
cd6b1fb
isTRUE
samuel-marsh Oct 27, 2023
d5a13a8
isTRUE
samuel-marsh Oct 27, 2023
ca2a363
isTRUE
samuel-marsh Oct 27, 2023
32a00cf
isTRUE
samuel-marsh Oct 27, 2023
c034430
isTRUE
samuel-marsh Oct 27, 2023
367c2e3
isTRUE
samuel-marsh Oct 27, 2023
0ecb78b
update changelog
samuel-marsh Oct 27, 2023
ad66e37
fix error
samuel-marsh Oct 27, 2023
a900114
Update vignettes for release
samuel-marsh Oct 27, 2023
93d1eb7
update changelog
samuel-marsh Oct 27, 2023
9811425
bump version
samuel-marsh Oct 27, 2023
6e1d2d6
fix dual assay slot error
samuel-marsh Oct 30, 2023
4efd6e4
remove testing code
samuel-marsh Oct 30, 2023
e448353
update vignette
samuel-marsh Oct 30, 2023
a4b5577
update vignette
samuel-marsh Oct 30, 2023
d00bc1d
typo
samuel-marsh Oct 31, 2023
aecbcc2
fix cell qc
samuel-marsh Oct 31, 2023
4b0db2a
list naming fix
samuel-marsh Oct 31, 2023
9dff582
fix list naming
samuel-marsh Oct 31, 2023
1731b4f
fix list naming
samuel-marsh Oct 31, 2023
4ca1f26
add split to histogram
samuel-marsh Oct 31, 2023
905e563
update import
samuel-marsh Oct 31, 2023
c9a8db9
update docs
samuel-marsh Oct 31, 2023
9cca3cf
update vignettes with new functionality/capatibility
samuel-marsh Oct 31, 2023
4acd80c
update changelog
samuel-marsh Oct 31, 2023
157e4e0
bump version and date
samuel-marsh Oct 31, 2023
4718a2d
update vignette
samuel-marsh Nov 1, 2023
a08bcd5
bump version and date
samuel-marsh Nov 1, 2023
74a1d42
fix dont run qc function in package build
samuel-marsh Nov 1, 2023
74824e3
add parameter definition
samuel-marsh Nov 1, 2023
07fce4e
fix doi link
samuel-marsh Nov 1, 2023
c52494e
import layers needed?
samuel-marsh Nov 1, 2023
d52e349
update imports remove layers
samuel-marsh Nov 1, 2023
6e567b9
update docs
samuel-marsh Nov 1, 2023
a1294d3
call seurat for data object
samuel-marsh Nov 1, 2023
9a3b857
fix tests
samuel-marsh Nov 1, 2023
6edbf07
fix plot mappings
samuel-marsh Nov 1, 2023
fab6bb8
fix bindings in filter
samuel-marsh Nov 1, 2023
456f4d8
fix line length
samuel-marsh Nov 1, 2023
3a14ff7
update docs
samuel-marsh Nov 1, 2023
f5320f6
fix retrieval of ieg list
samuel-marsh Nov 1, 2023
cf6fced
fix ieg again
samuel-marsh Nov 1, 2023
287d1e4
typo
samuel-marsh Nov 1, 2023
c273180
fix return
samuel-marsh Nov 1, 2023
ab24218
fix docs
samuel-marsh Nov 1, 2023
e71374d
update ieg
samuel-marsh Nov 1, 2023
720bdba
redo retrieval
samuel-marsh Nov 1, 2023
7ff0b6d
bump version
samuel-marsh Nov 1, 2023
d5aefa1
Update data
samuel-marsh Nov 1, 2023
9f34a92
update gene list
samuel-marsh Nov 1, 2023
6fd0542
replace data
samuel-marsh Nov 1, 2023
2539cbf
fix
samuel-marsh Nov 1, 2023
4c4d459
bump version
samuel-marsh Nov 1, 2023
4f88beb
add new gene lists to rsysdata
samuel-marsh Nov 1, 2023
e262097
typo
samuel-marsh Nov 1, 2023
9cd1ddb
bump version
samuel-marsh Nov 1, 2023
c24d1dd
reorg
samuel-marsh Nov 3, 2023
5531560
figure plot add
samuel-marsh Nov 3, 2023
fc61cbc
test add figure plot
samuel-marsh Nov 3, 2023
8a26ed2
typo
samuel-marsh Nov 3, 2023
2e8e628
update docs
samuel-marsh Nov 3, 2023
36e01d4
figure plot
samuel-marsh Nov 3, 2023
6e37587
fix figure plot multiple features
samuel-marsh Nov 3, 2023
3a1adbd
bump news
samuel-marsh Nov 3, 2023
d2e6ca8
bump version and date
samuel-marsh Nov 3, 2023
a7d1a66
fix plot returns
samuel-marsh Nov 3, 2023
9433a88
depend SeuratObject 5.0.0
samuel-marsh Nov 6, 2023
703b142
just update min version
samuel-marsh Nov 6, 2023
3ce41af
update imports
samuel-marsh Nov 6, 2023
16e3d25
update NAMESPACE
samuel-marsh Nov 6, 2023
f2e83d8
bump version and date
samuel-marsh Nov 6, 2023
7de5a6e
test site build
samuel-marsh Nov 6, 2023
dcfc692
test site build
samuel-marsh Nov 6, 2023
b18cf80
update index
samuel-marsh Nov 6, 2023
e6c8fbc
update changelog
samuel-marsh Nov 6, 2023
a751695
bump version
samuel-marsh Nov 6, 2023
abd468a
update cran comments
samuel-marsh Nov 6, 2023
709e3a5
update cran comments
samuel-marsh Nov 6, 2023
979fd06
remove liger temp
samuel-marsh Nov 6, 2023
d32ca0a
fix doi citation
samuel-marsh Nov 6, 2023
913ff6b
cran comments
samuel-marsh Nov 6, 2023
8ad512b
re add rliger
samuel-marsh Nov 6, 2023
dc50ff3
update docs
samuel-marsh Nov 8, 2023
c4a36bb
temp remove liger dep functions
samuel-marsh Nov 8, 2023
d560597
remove liger suggests
samuel-marsh Nov 8, 2023
239155e
update changelog
samuel-marsh Nov 8, 2023
9adba6c
bump date
samuel-marsh Nov 8, 2023
6c43258
proper magrittr import
samuel-marsh Nov 8, 2023
8240eac
fix magrittr
samuel-marsh Nov 8, 2023
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samuel-marsh committed Nov 3, 2023

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commit d2e6ca8c7ccaa9e595ee999594b63a611321cbd2
4 changes: 2 additions & 2 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -2,8 +2,8 @@ Package: scCustomize
Type: Package
Title: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430>.
Version: 1.9.9.9039
Date: 2023-11-01
Version: 1.9.9.9040
Date: 2023-11-03
Authors@R: c(
person(given = "Samuel", family = "Marsh", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3012-6945")),
person(given = "Ming", family = "Tang", role = c("ctb"), email = "[email protected]"),