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Merged
brgew merged 212 commits into from
Jun 3, 2025
Merged

Develop #758

brgew merged 212 commits into from
Jun 3, 2025

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@brgew
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@brgew brgew commented Jun 3, 2025

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brgew added 30 commits December 5, 2022 17:01
@brgew
Minor efficiency modification to detect_genes().
b2e9b6b
@brgew
BPCells integration, part 1.
87b5750
@brgew
Incremental progress in integrating BPCells.
6ff92d6
@brgew
Incremental progress integrating BPCells matrices.
d92086e
@brgew
Incremental progress in integrating BPCells.
cf6e872
@brgew
Update Github Actions workflow.
4c13ce8
@brgew
Update Github Actions workflow.
86922c7
@brgew
Incremental progress integrating BPCells.
a37130e
@brgew
Incremental progress integrating BPCells into Monocle3.
8ffbdc2
@brgew
Incremental progress integrating BPCells into Monocle3.
cd55900
@brgew
Update tests file.
84ae924
@brgew
Incremental progress integrating BPCells.
db0a188
@brgew
Incremental progress integrating BPCells.
c83893e
@brgew
Incremental progress integrating BPCells.
dfddcc0
@brgew
Fix sparse matrix test.
ab42f68
@brgew
Incremental progress integrating BPCells.
e7fef28
@brgew
Incremental progress integrating BPCells.
59fccdc
@brgew
Incremental progress integrating BPCells.
ede2980
@brgew
Modify load_mm_data to use BPCells::import_matrix_market.
6a650cb
@brgew
Add BPCells binarization to utils.R: normalized_counts.
70cbf46
@brgew
Roll back change for binary norm_method with BPCells for now.
e33af8d
@brgew
Incremental progress integrating BPCells.
4fae3d4
@brgew
Fix github actions script.
4171705
@brgew
Fixes in utils.R
516316f
@brgew
Incremental progress integrating BPCells.
eeb82b1
@brgew
Incremental progress integrating BPCells.
ce4546e
@brgew
Fix regression test.
a604091
@brgew
Incremental progress integrating BPCells.
1fc10ab
@brgew
Incremental progress integrating BPCells.
72c0890
@brgew
Incremental progress integrating BPCells.
70d76bb
brgew and others added 25 commits May 24, 2024 12:33
@brgew
Update Github Actions to use Docker image v1.4.18_1.
c8587c5
@brgew
Update regression tests for new Docker image: 1.4.18_1.
d119ecb
@brgew
Another regression test update for new Docker image: 1.4.18_1.
b182cb5
@rfriedman22
Fix tock to always convert difftime to secs. Previous implementation …
8379894 
…was misleading if the difftime was >60s
@brgew
Fix typo.
4309252
@brgew
Merge branch 'develop' of https://github.com/cole-trapnell-lab/monocle3…
040397b 
… into develop
@brgew
Fix fix_missing_cell_labels() when no cells need fixing.
eed1cd6
@rfriedman22
Allow plot_cells_per_sample_and_perturbation to optionally zscore cou…
7ad8299 
…nts before plotting
@rfriedman22
Drawing a cutoff in plot_cells_per_sample_and_perturbation is now opt…
dbf4b46 
…ional
@brgew
Update BPCells installation instructions.
de6f4c9
@rfriedman22
Update UMI plotting to allow for Z-score based cutoff
a0532b5
@brgew
Add tar version notes to save_monocle_objects() and save_transform_mo…
03f05ea 
…dels().
@ctrapnell
Don't force progress bar for accessory functions
7b05c87
@ctrapnell
Merge branch 'develop' of github.com:cole-trapnell-lab/monocle3 into …
a2017a2 
…develop
@maddyduran
allow for gene_group_df with one grouping in aggregate_gene_expression
9fe2be2
@brgew
Fix row order matrix transpose temp matrix path.
17b4f66
@brgew
Update version.
ce2af4b
@rfriedman22
Update remotes path of BPCells
de92e4e
@rfriedman22
Add our speedglm to DESCRIPTION
3c0b2c9
@rfriedman22
Fix weird indents in DESCRIPTION
2b7a19c
@rfriedman22
Faster implementation of aggregating genes (#742)
dab9323 
Aggregate genes using a similar method as cells, but allowing for the possibility that a gene can belong to multiple aggregation groups.
@brgew
Add global variable that disables some preprocess_method value checks…
9b70d42 
… in reduce_dimension().
@brgew
Increment version.
0ae876a
@brgew
Fix error in graph_test() on R 4.5.0.
64a996a
@brgew
Remove requirement that matrix_control list be given in convert_count…
501aecb 
…s_matrix call.
@brgew brgew requested review from ctrapnell and hpliner as code owners June 3, 2025 23:00
@brgew brgew self-assigned this Jun 3, 2025
@brgew brgew merged commit 064ab35 into master Jun 3, 2025
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@ctrapnell ctrapnell Awaiting requested review from ctrapnell ctrapnell is a code owner

@hpliner hpliner Awaiting requested review from hpliner hpliner is a code owner

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5 participants

@brgew @ctrapnell @rfriedman22 @maddyduran