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dpeerlab
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SEACells
SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
GNU General Public License v2.0
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Error when model.construct_kernel_matrix: can SEACells be applied in python command line, not just in Jupyter?
#71
LiuCanidk
opened
5 days ago
0
How to run SEACells efficiently on large-scale dataset
#70
koh2ng0
opened
1 month ago
1
What is the actual formula to construct the affinity kernel matrix?
#69
caodudu
opened
1 month ago
1
minor adjustment for load_transcripts function
#68
Huangy57
opened
2 months ago
0
requirements.txt file contains incorrect versions numbers
#67
nbtm-sh
opened
2 months ago
0
CUDA error while running "model.fit"
#66
NekoClaviS
opened
4 months ago
0
Spurious metacell
#65
yxsee
opened
4 months ago
0
Bump tqdm from 4.64 to 4.66.3
#64
dependabot[bot]
opened
4 months ago
0
The data cannot be downloaded
#63
cfzgg
opened
4 months ago
1
Circular import and GPU version
#62
GLking123
closed
4 weeks ago
1
Handling metacell creation for rare cell types (<< 75 cells)
#61
uqzqiao
opened
4 months ago
0
maxFragmentLength=147
#60
Aya-Balbaa
opened
5 months ago
0
Custom Neighborhood Graph for Metacells
#59
shahrozeabbas
opened
5 months ago
0
No speed increase was observed when use_gpu=True
#58
OMIC-coding
opened
5 months ago
1
Aggregation of expression data ends up in matrix filled with NaN's
#57
zvittorio
opened
7 months ago
5
Scale or not scale be more suitable for computation of SEACells?
#56
NPTL1201
opened
8 months ago
0
conda environment yaml file dependency seems conflict
#55
shiqi-yang
closed
8 months ago
1
wonder why the @parm `ceiling` can be set to 10^9
#54
chenc327
opened
10 months ago
0
[Question] Algorithm for PWM computation
#53
josephineyates
opened
10 months ago
0
Fail to install seacells via conda due to conflicts in environment.yaml
#52
ChangSuBiostats
opened
11 months ago
2
Update requirements.txt
#51
arhowe00
closed
11 months ago
0
The data cannot be downloaded
#50
hai178912522
closed
1 year ago
1
cell-cell affinity matrix
#49
ytliu01
opened
1 year ago
1
Reproducibility issue
#48
evaham1
opened
1 year ago
2
PWM for mouse genome
#47
torkencz
closed
1 year ago
1
Renaming the Seacells
#46
Gavin-Lijy
opened
1 year ago
1
Add pre-commit hooks
#45
WeilerP
closed
1 year ago
0
Add pre-commit hooks
#44
WeilerP
closed
1 year ago
0
Many cells have zero non-trivial (>0.1) assignments
#43
simozhou
opened
1 year ago
1
PWM.h5ad in SEACells/notebooks/SEACell_tf_activity.ipynb
#42
roshan9128
closed
1 year ago
2
Issue with model.initialize_archetypes()
#41
iamsalil
opened
1 year ago
4
Computing SEACells on individual samples
#40
learning-MD
closed
1 year ago
1
Way too strict dependency pins
#39
Zethson
opened
1 year ago
3
RuntimeError: cannot cache function 'sparse_mean_var_minor_axis'
#38
simozhou
closed
1 year ago
2
ValueError: row, column, and data array must all be the same length when running model.fit
#37
tatyana-perlova
closed
1 year ago
3
ArchR code tutorial - addGroupCoverage has no maxFragmentLength param
#36
simozhou
closed
1 year ago
0
Peak calling on NFR fragments
#35
ivanferrreira
closed
1 year ago
4
MemoryError when fitting model.fit
#34
tatyana-perlova
opened
1 year ago
10
R version of SEACells
#33
zji90
closed
1 year ago
1
Reproducible example for the PBMC dataset
#32
lebf3
closed
1 year ago
1
Issue with cupyx
#31
jindalk
closed
1 year ago
4
Cannot initialize_archetypes
#30
GuiSeSanz
closed
1 year ago
3
Bump joblib from 1.1 to 1.2.0
#29
dependabot[bot]
closed
10 months ago
0
Bump certifi from 2021.10.8 to 2022.12.7
#28
dependabot[bot]
closed
1 year ago
1
Add option to define peak annotations using pyranges
#27
jordanc17
closed
1 year ago
0
Save Model
#26
Sayyam-Shah
closed
1 year ago
2
SeaCells analysis for each cell type
#25
fl-yu
closed
1 year ago
1
Gene-peak association fails with Cellranger GTF file
#24
jordanc17
closed
1 year ago
0
gene score matrix with sparse format
#23
fl-yu
closed
1 year ago
1
Multiome Dataset
#22
Sayyam-Shah
closed
1 year ago
4
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