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Seurat v4.0.2 #4529

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May 24, 2021
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12e42bc
Add lsiproject option
timoast Nov 9, 2020
c3289b0
Add rlsi option
timoast Nov 10, 2020
b1cfc66
Rename cells in weight.reduction to match query
timoast Nov 11, 2020
757c7d7
fix weight.reduction parameter validation for transfer
timoast Nov 11, 2020
eaf5e50
Fix weighting when dims not supplied
timoast Nov 11, 2020
bc53f6e
Set reuse.weight.matrix to F if not stored
timoast Nov 11, 2020
5b4c46d
Fix weight.reduction for integration anchors
timoast Nov 12, 2020
dea207d
Pull formals from specific method
timoast Nov 12, 2020
b5beded
Enable LSI projection in TransferData
timoast Nov 12, 2020
c1ed7c6
Fix object name
timoast Nov 16, 2020
84d085d
Merge branch 'release/4.0.0' into feat/lsi_project
timoast Nov 30, 2020
4e451ff
Add lsiproject docs
timoast Nov 30, 2020
2b6bbb9
Avoid using dense matrix when creating dummy assay
timoast Dec 2, 2020
d35ebde
Merge branch 'release/4.0.0' of github.com:satijalab/seurat into rele…
timoast Dec 18, 2020
a117a9f
Clarify requirements for metadata; #3838
timoast Dec 18, 2020
fda1794
Merge branch 'release/4.0.0' into feat/lsi_project
timoast Jan 7, 2021
9371be5
Updated singlecellexperiment
torkencz Jan 11, 2021
7493dc4
Divide by sigma for LSI projection
timoast Jan 14, 2021
8e85cea
Add rpca option for FindTransferAnchors
timoast Jan 14, 2021
d80ccfe
Update docs
timoast Jan 14, 2021
9bd6e98
Merge branch 'release/4.0.0' into feat/lsi_project
timoast Jan 15, 2021
9dca205
Merge branch 'release/4.0.0' into feat/lsi_project
timoast Jan 15, 2021
79872c5
Merge remote-tracking branch 'private/release/4.0.0' into feat/lsi_pr…
timoast Jan 15, 2021
4532c0c
Fix typo
timoast Jan 15, 2021
86ee295
Add scale parameter to FindTransferAnchors
timoast Jan 20, 2021
c3308a1
Merge branch 'release/4.0.0' into feat/lsi_project
timoast Jan 20, 2021
97cd409
Merge branch 'release/4.0.0' into feat/lsi_project
timoast Jan 20, 2021
9e8ee22
Merge branch 'release/4.0.0' into feat/lsi_project
yuhanH Jan 24, 2021
4fe29c8
Merge branch 'release/4.0.0' into feat/lsi_project
timoast Jan 25, 2021
fdaeb4c
Merge branch 'develop' into as_singlecell_experiment_update
andrewwbutler Feb 3, 2021
114d998
Merge branch 'develop' into feat/lsi_project
andrewwbutler Feb 3, 2021
b04406b
Merge branch 'develop' into feat/lsi_project
yuhanH Feb 5, 2021
d918f6b
fix the bug when set reference.reduction
yuhanH Feb 6, 2021
a71efb7
Merge branch 'develop' into feat/lsi_project
timoast Feb 9, 2021
5fe86c6
Merge branch 'develop' into feat/lsi_project
timoast Feb 10, 2021
e756e5f
Scale using reference stats for rpca
timoast Feb 10, 2021
1fb8757
Remove parameter
timoast Feb 10, 2021
b5cb48b
Set anchor.features for rlsi
timoast Feb 12, 2021
a2e84a7
Merge branch 'develop' into as_singlecell_experiment_update
timoast Feb 12, 2021
2ac7230
Enable lsiproject option in MapQuery
timoast Feb 15, 2021
bc5b319
Merge branch 'develop' into feat/lsi_project
timoast Feb 15, 2021
7b3d7e3
Change to more descriptive variable names
timoast Feb 15, 2021
45d8208
Fix L2 norm for rpca
timoast Feb 16, 2021
037236b
add rpca.ref rpca name
yuhanH Feb 16, 2021
9824feb
rpca l2
yuhanH Feb 16, 2021
fa18832
fix rpca ref and query flip
yuhanH Feb 16, 2021
2cef300
warning for reference reduction assay
yuhanH Feb 17, 2021
c9c0212
Don't rescale query with reference stats for rpca
timoast Feb 18, 2021
57eeb29
Allow specifying custom weight.reduction and reductions in MapQuery
timoast Feb 18, 2021
6d842b3
add pcaproject and rpca scale
yuhanH Feb 19, 2021
151ebb0
Merge branch 'develop' into as_singlecell_experiment_update
torkencz Feb 19, 2021
fc85764
Update objects.R
torkencz Feb 19, 2021
7687ae0
switch reduction and reduction.2
yuhanH Feb 23, 2021
75fd995
reset parameters
yuhanH Feb 23, 2021
aec88a1
trim lsi dims
yuhanH Feb 26, 2021
bd44ed1
Merge branch 'develop' into feat/lsi_project
yuhanH Feb 26, 2021
c592466
wrote PlotPerturbScore2 to account for datasets with multiple cell types
epapalexi Mar 12, 2021
c1930f5
Merge branch 'develop' into feat/lsi_project
timoast Mar 16, 2021
f8ee295
Update description and changelog
timoast Mar 16, 2021
d6ea9f3
updated feature meta
torkencz Mar 18, 2021
291cea2
Merge branch 'develop' into as_singlecell_experiment_update
torkencz Mar 18, 2021
9e4e502
fix FC calculation under non-default normalization methods
andrewwbutler Mar 19, 2021
4bb5df1
minor style tweaks
andrewwbutler Mar 19, 2021
264aca5
fix 1 gene bug
andrewwbutler Mar 19, 2021
312f7ba
Merge branch 'develop' into mix_fix
andrewwbutler Mar 19, 2021
aa2c4b0
more drop fixes for single gene
andrewwbutler Mar 19, 2021
b483c75
minor fix to label nt class properly in perturbation score df
epapalexi Mar 19, 2021
bf0c51d
Add function to read in and add Azimuth scores to a Seurat object
mojaveazure Mar 19, 2021
c430468
Bump develop version
mojaveazure Mar 19, 2021
54afea4
Update changelog
mojaveazure Mar 19, 2021
8e19e4b
check normalization.method
andrewwbutler Mar 19, 2021
4860c03
plotting the correct density distributions when split.by is set
epapalexi Mar 19, 2021
09ffb80
Alt exp test
torkencz Mar 19, 2021
17ff54a
minor fix
andrewwbutler Mar 22, 2021
9e2b598
Fix score.thresh parameter in ScoreJackStraw.Seurat
colganwi Mar 22, 2021
163b037
Fix feature names
timoast Mar 22, 2021
71769be
Add link to SCE
timoast Mar 22, 2021
6b985d2
Update release notes and dev version
timoast Mar 22, 2021
07b00fc
Fix release notes
timoast Mar 22, 2021
f2b7794
Merge pull request #494 from satijalab/as_singlecell_experiment_update
andrewwbutler Mar 23, 2021
15e7a33
Merge branch 'develop' into feat/AzimuthScores
andrewwbutler Mar 23, 2021
a860926
Merge pull request #544 from satijalab/feat/AzimuthScores
mojaveazure Mar 23, 2021
62baa86
Merge branch 'develop' into fix/FindMarkers_FC
andrewwbutler Mar 24, 2021
73d17e9
add shuffle param to FeatureScatter
samuel-marsh Mar 24, 2021
2083861
Merge branch 'develop' into feat/lsi_project
yuhanH Mar 25, 2021
4937f2b
coreect reduction ref query order
yuhanH Mar 25, 2021
6c4ae04
allow project.query option in rpca
yuhanH Mar 25, 2021
74708f8
cca mapquery
yuhanH Mar 26, 2021
ff36706
correctly handle DimReduc case
andrewwbutler Mar 31, 2021
b577add
Merge branch 'develop' of github.com:satijalab/seurat into patch-1
andrewwbutler Mar 31, 2021
d849ed1
bump version, update NEWS
andrewwbutler Mar 31, 2021
8df8249
Merge pull request #4268 from colganwi/patch-1
andrewwbutler Mar 31, 2021
e298178
Merge branch 'develop' of github.com:satijalab/seurat into feature-sc…
andrewwbutler Mar 31, 2021
40f6b72
run docs, bump version, update NEWS
andrewwbutler Mar 31, 2021
7367ae0
Merge pull request #4280 from samuel-marsh/feature-scatter_shuffle
andrewwbutler Mar 31, 2021
b9de4ce
Merge branch 'develop' into fix/FindMarkers_FC
Mar 31, 2021
379a545
add compatability for updated umap-learn package
andrewwbutler Apr 2, 2021
780363a
version check should be >=
andrewwbutler Apr 2, 2021
61fd372
bump version, update NEWS
andrewwbutler Apr 2, 2021
043c416
Merge pull request #543 from satijalab/fix/FindMarkers_FC
andrewwbutler Apr 2, 2021
07aae52
fix azimuth link
andrewwbutler Apr 3, 2021
4921fb3
Merge branch 'develop' into fix/umap-learn-versions
mojaveazure Apr 3, 2021
f96af40
Merge pull request #547 from satijalab/fix/link
andrewwbutler Apr 4, 2021
daad8d6
Merge branch 'master' into develop
andrewwbutler Apr 4, 2021
79bb026
Merge branch 'develop' into fix/umap-learn-versions
andrewwbutler Apr 4, 2021
1ba54ff
bump version, update news
andrewwbutler Apr 4, 2021
8a863fb
Merge pull request #546 from satijalab/fix/umap-learn-versions
andrewwbutler Apr 5, 2021
4b14fdf
Merge branch 'develop' into feat/lsi_project
timoast Apr 5, 2021
70288b7
Fix dimensionality parameter in FindNN
timoast Apr 5, 2021
a90d6aa
Set LogNormalize for LSI
timoast Apr 6, 2021
65cf860
Update docs
timoast Apr 6, 2021
bf3b532
Change slot access, improve documentation
timoast Apr 6, 2021
ff407f5
Update docs
timoast Apr 6, 2021
32a49a6
Improve docs for transfer
timoast Apr 6, 2021
e59716d
fix vignette comment
andrewwbutler Apr 9, 2021
30bfbce
stop FindMarkers if ident.1 is empty
jaisonj708 Apr 9, 2021
a54c00a
Fix DotPlot to use log1p when scale=False. Fixes https://github.com/s…
saketkc Apr 9, 2021
52dc13f
var name fixes
andrewwbutler Apr 12, 2021
8bebac7
use design matrices for perturb sigs
jaisonj708 Apr 12, 2021
df18981
Merge pull request #549 from satijalab/fix/vignette_comment
andrewwbutler Apr 12, 2021
982ec4c
Merge branch 'master' into develop
andrewwbutler Apr 12, 2021
7c9de56
imports
jaisonj708 Apr 12, 2021
61748cb
Update release notes
timoast Apr 12, 2021
c296238
Add warning message for SCT normalization for rlsi
timoast Apr 12, 2021
3d16da8
Merge branch 'develop' into feat/lsi_project
timoast Apr 12, 2021
f5e02b2
Update develop version
timoast Apr 12, 2021
a22ca5d
Merge branch 'feat/lsi_project' of github.com:satijalab/seurat-privat…
timoast Apr 12, 2021
a5f0c5c
Merge pull request #496 from satijalab/feat/lsi_project
timoast Apr 13, 2021
92fe0b8
Merge branch 'develop' into feat/fasterPerturbSig
jaisonj708 Apr 14, 2021
6decdb3
Merge branch 'develop' into fix/dotplot
mojaveazure Apr 14, 2021
6d407be
Merge pull request #551 from satijalab/fix/dotplot
saketkc Apr 14, 2021
d7a383a
fix shuffle
yuhanH Apr 16, 2021
d1e9769
Merge branch 'develop' into feat/fasterPerturbSig
epapalexi Apr 19, 2021
d731246
Merge pull request #552 from satijalab/feat/fasterPerturbSig
epapalexi Apr 19, 2021
f268cf1
Remove outdated comments; #4393
timoast Apr 22, 2021
3f4a53f
Merge branch 'develop' into fix/shuffle_DimPlot
yuhanH Apr 23, 2021
05e3b72
Merge branch 'develop' into fix/FindMarkers
jaisonj708 Apr 23, 2021
d2088f8
adding target.gene.class parameter to specify metadata column with ta…
epapalexi Apr 23, 2021
d4b80f4
Merge branch 'develop' into mix_fix
epapalexi Apr 23, 2021
c94d352
Merge pull request #554 from satijalab/doc/mastde
mojaveazure Apr 26, 2021
672f855
Merge branch 'develop' into fix/shuffle_DimPlot
mojaveazure Apr 26, 2021
500edf4
Bump develop version
mojaveazure Apr 26, 2021
7c12215
Update changelog
mojaveazure Apr 26, 2021
42374b1
Merge branch 'develop' into mix_fix
mojaveazure Apr 26, 2021
ee832e1
Merge pull request #553 from satijalab/fix/shuffle_DimPlot
mojaveazure Apr 26, 2021
30f4bd4
Merge branch 'develop' into mix_fix
mojaveazure Apr 26, 2021
c68fa80
added missing documentation entries
epapalexi Apr 26, 2021
6eb0271
Merge branch 'mix_fix' of github.com:satijalab/seurat-private into mi…
epapalexi Apr 26, 2021
eeadf34
prevent future seed warnings
andrewwbutler Apr 28, 2021
3f9b32f
Merge branch 'develop' into fix/future_warnings
andrewwbutler Apr 29, 2021
2d9b487
add AddAzimuthResults
jaisonj708 Apr 30, 2021
c83ca46
fixed bug in MixscapeHeatmap for order.by.prob=F
epapalexi May 4, 2021
80b971f
Merge branch 'develop' into fix/FindMarkers
andrewwbutler May 5, 2021
2d2ec41
update NEWS, bump version
andrewwbutler May 5, 2021
34c6372
Merge pull request #550 from satijalab/fix/FindMarkers
andrewwbutler May 6, 2021
c34e320
fix range shift when labeling GeomSpatial plots
andrewwbutler May 6, 2021
a310886
Bump develop version
mojaveazure May 6, 2021
c3bc3d5
Merge pull request #560 from satijalab/fix/GeomSpatial_range
mojaveazure May 7, 2021
5a3c44e
Merge branch 'develop' into feat/AddAzimuthResults
jaisonj708 May 7, 2021
6df30db
Merge branch 'develop' into fix/future_warnings
timoast May 10, 2021
c4ba52c
fix spatial plots for non-square images
andrewwbutler May 11, 2021
3bf740f
update mixscape vignette with new parameter name
andrewwbutler May 12, 2021
04e4663
Merge branch 'develop' into mix_fix
andrewwbutler May 12, 2021
5108128
Fix missing import for layer_scales in LabelClusters
mojaveazure May 13, 2021
fcd23c7
bump version, update NEWS
andrewwbutler May 13, 2021
c07b8b2
Merge pull request #561 from satijalab/fix/SpatialPlot
andrewwbutler May 13, 2021
45ccb8f
Merge branch 'develop' into fix/future_warnings
andrewwbutler May 13, 2021
ccce60b
bump version, update NEWS
andrewwbutler May 13, 2021
f7ec70b
Merge pull request #557 from satijalab/fix/future_warnings
mojaveazure May 14, 2021
7cd62d6
Pass fc.name parameter; #4474
timoast May 14, 2021
0a4656f
Merge branch 'develop' into fix/fcname
mojaveazure May 14, 2021
71b834e
Bump develop version
mojaveazure May 14, 2021
9b082a5
Merge pull request #562 from satijalab/fix/fcname
mojaveazure May 14, 2021
3f09a32
Merge branch 'develop' into feat/AddAzimuthResults
andrewwbutler May 17, 2021
02205f2
minor style adjustments
andrewwbutler May 17, 2021
c977212
update NEWS, bump version
andrewwbutler May 17, 2021
46b9f0f
Merge pull request #559 from satijalab/feat/AddAzimuthResults
andrewwbutler May 18, 2021
568aa65
prep release 4.0.2
andrewwbutler May 18, 2021
b28a089
deprecate parameter, style tweaks
andrewwbutler May 19, 2021
ef6833f
Merge branch 'develop' into mix_fix
andrewwbutler May 19, 2021
963a12a
update NEWS, bump version
andrewwbutler May 19, 2021
d794e8e
fix background for SpatialPlots
andrewwbutler May 19, 2021
833a1ae
Merge pull request #556 from satijalab/mix_fix
andrewwbutler May 19, 2021
b197841
Merge branch 'develop' into release/4.0.2
andrewwbutler May 20, 2021
c3b4a6b
Update maintainer email
mojaveazure May 20, 2021
6597b07
Update CRAN comments
mojaveazure May 20, 2021
114c5b9
Merge pull request #563 from satijalab/release/4.0.2
mojaveazure May 20, 2021
058325f
Fix typo in tests
mojaveazure May 20, 2021
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6 changes: 3 additions & 3 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: Seurat
Version: 4.0.1.9015
Date: 2021-05-19
Version: 4.0.2
Date: 2021-05-20
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Authors@R: c(
Expand All @@ -10,7 +10,7 @@ Authors@R: c(
person(given = "Jeff", family = "Farrell", email = "jfarrell@g.harvard.edu", role = "ctb"),
person(given = "Christoph", family = "Hafemeister", email = "chafemeister@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-6365-8254")),
person(given = "Yuhan", family = "Hao", email = "yhao@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-1810-0822")),
person(given = "Paul", family = "Hoffman", email = "nygcSatijalab@nygenome.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7693-8957")),
person(given = "Paul", family = "Hoffman", email = "seurat@nygenome.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7693-8957")),
person(given = "Jaison", family = "Jain", email = "jjain@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-9478-5018")),
person(given = "Efthymia", family = "Papalexi", email = "epapalexi@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-5898-694X")),
person(given = "Patrick", family = "Roelli", email = "proelli@nygenome.org", role = "ctb"),
Expand Down
2 changes: 1 addition & 1 deletion NEWS.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Seurat develop
# Seurat 4.0.2 (2020-03-20)
## Added
- New `AddAzimuthScores()` and `AddAzimuthResults()` functions
- Add `shuffle` parameter to `FeatureScatter()` ([#4280](https://github.com/satijalab/seurat/pull/4280))
Expand Down
2 changes: 1 addition & 1 deletion R/visualization.R
Original file line number Diff line number Diff line change
Expand Up @@ -7601,7 +7601,7 @@ SingleSpatialPlot <- function(
}
plot <- plot + scale
}
plot <- plot + NoAxes()
plot <- plot + NoAxes() + theme(panel.background = element_blank())
return(plot)
}

Expand Down
8 changes: 4 additions & 4 deletions cran-comments.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Seurat v4.0.1
# Seurat v4.0.2

## Test environments
* local Ubuntu 18.04.4 install, R 4.0.3
Expand All @@ -14,8 +14,8 @@ There were no ERRORs, WARNINGs, or NOTEs

## Downstream dependencies

There are no packages that depend on Seurat.
There is one package that depends on Seurat: tidyseurat; this update does not impact its functionality

There are six packages that imports Seurat: CDSeq, DUBStepR, scMappR, Signac, SignacX, and SoupX; this update does not impact their functionality
There are seven packages that imports Seurat: CDSeq, DUBStepR, rPanglaoDB, scMappR, Signac, SignacX, and SoupX; this update does not impact their functionality

There are eleven packages that suggest Seurat: BisqueRNA, clustree, conos, DIscBIO, dyngen, nanny, rliger, Rmagic, singleCellHaystack, treefit, VAM; this update does not impact their functionality.
There are nine packages that suggest Seurat: BisqueRNA, ClustAssess, clustree, conos, DIscBIO, dyngen, rliger, Rmagic, VAM; this update does not impact their functionality.