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aertslab
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scenicplus
SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Problem with TSS
#474
ReviewBrandLab2024
opened
4 days ago
0
scenicplus prepare_data prepare_menr error
#470
Yiming-Huang-neuron
opened
1 week ago
2
Understanding scenicPlus settings and Outputs
#469
orian116
opened
1 week ago
0
Error when running SnakeMake
#468
gilgolan73
opened
1 week ago
0
Problems with importing for new, Tutorial: Perturbation simulation
#467
finncreeggan
opened
2 weeks ago
1
Re-calculating enrichment scores after filtering eRegulons and "+"/ "-" eRegulon signs
#466
maithermbarros
opened
2 weeks ago
3
create_cistopic_object_from_fragments run forever
#465
Quentin-bioinfo
closed
2 weeks ago
0
Creating custom cistarget database
#462
zznx
opened
3 weeks ago
0
Issue while Installing on Fedora HPC Using conda environment
#461
Stack7
opened
3 weeks ago
3
Error in rule eGRN_extended - ValueError: No objects to concatenate
#460
maithermbarros
closed
2 weeks ago
2
Pycistopic Temporary Fragment file cannot be found
#458
yrsong001
opened
3 weeks ago
1
Re-running old SCENIC+ pipeline in the new version without snakemake
#457
skoturan
closed
2 weeks ago
2
Update perturbation simulation
#456
SeppeDeWinter
closed
1 month ago
0
SCENIC+ crashed in tf_to_gene step
#454
kangjiajinlong
opened
1 month ago
3
how much resource needed? Multiome datasets with 270k cells
#453
JinKyu-Cheong
closed
1 month ago
1
Input annotated 10x Multiome Seurat object into SCENIC+
#452
strawberry098
closed
1 month ago
1
Region set, scores.feather and NameError: name 'run_cgs_models_mallet
#451
strawberry098
opened
1 month ago
3
QC files are not formed
#450
gilgolan73
closed
1 week ago
5
`ValueError: No objects to concatenate` during `motif_enrichment_dem` Execution
#449
OjongTabi
opened
1 month ago
1
How can I convert a SCENIC+ object to a loom file?
#448
uqnsarke
opened
1 month ago
0
Count matrix to cistopic link broken + scalability to large datasets question
#447
wgao688
opened
1 month ago
4
TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
#446
kangjiajinlong
closed
1 month ago
3
"enable_string_cache()" in export_pseudobulk using tutorial data
#445
gilgolan73
closed
1 month ago
1
SCENIC+ prepare_menr error: TypeError unbound method set.union() needs an argument
#442
jklvrt
closed
1 month ago
7
pyscenic dependency
#441
wangjiawen2013
opened
2 months ago
1
Missing files for `scenicplus init_snakemake --out_dir`
#440
pavelToman
closed
1 month ago
2
Error in tf_to_gene
#439
MatthewTCManion
closed
1 month ago
6
error runing scenic+
#438
ACAIDI
opened
2 months ago
1
'PyRanges object has no attribute', 'Count'
#437
laki-spk
closed
2 months ago
1
pip installation issue
#436
swbujnowski
closed
2 months ago
3
Data base
#435
SteveTur
opened
2 months ago
3
how to prepare motif2tf file for `path_to_motif_annotations` in plant
#434
xuzhougeng
closed
1 month ago
2
Failing to integrate scATAC + scRNA cells (non multiome data). Error in rule prepare_GEX_ACC_non_multiome:
#433
twinklevhatkar
opened
2 months ago
1
TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
#432
degrainger
closed
2 months ago
3
run_cgs_models_mallet not working
#431
uqnsarke
opened
2 months ago
4
Where is genome_annotation.tsv ?
#429
Zhangruiqi111
closed
2 months ago
4
A simple little question
#428
goodstudy28
opened
2 months ago
1
.raw
#427
paupaiz
opened
3 months ago
0
Length mismatch when running get_search_space
#426
ytrink
closed
2 months ago
4
module load cluster/wice/bigmem
#425
Zhangruiqi111
closed
2 months ago
2
Original Cells Used for pseudomultiome
#423
orian116
opened
3 months ago
1
Avoid discarding cells if one modality failed.
#421
ktroule
opened
3 months ago
0
Branch missing scenicplus.cistromes modules
#418
AmosFong1
closed
2 months ago
5
ModuleNotFoundError: No module named 'scenicplus.dimensionality_reduction'
#417
dsecilmis
closed
1 month ago
1
Error when overlapping scRNA-seq annotations to cistopic_obj (argmax of an empty sequence)
#416
leahyekim
opened
3 months ago
6
Question: How to 'map' new SCENIC+ nomenclature with the older versions
#415
ccruizm
opened
3 months ago
0
How to open pkl file generated by old scenicplus package?
#414
AIBio
opened
3 months ago
5
TypeError: score_eRegulons() got an unexpected keyword argument 'scplus_obj'
#413
LukasOussoren
closed
1 month ago
2
run_pycistarget is not defined
#412
DmitriiSeverinov
closed
2 months ago
5
Clarification needed: Input_file for running snakemake pipieline?
#409
leahyekim
closed
4 months ago
2
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