aertslab scenicplus issues

aertslab / 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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issues

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Count matrix to cistopic link broken + scalability to large datasets question

#447 wgao688 opened 3 months ago
4
TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object

#446 kangjiajinlong closed 2 months ago
3
"enable_string_cache()" in export_pseudobulk using tutorial data

#445 gilgolan73 closed 3 months ago
1
SCENIC+ prepare_menr error: TypeError unbound method set.union() needs an argument

#442 jklvrt closed 3 months ago
7
pyscenic dependency

#441 wangjiawen2013 opened 3 months ago
1
Missing files for `scenicplus init_snakemake --out_dir`

#440 pavelToman closed 2 months ago
2
Error in tf_to_gene

#439 MatthewTCManion closed 3 months ago
6
error runing scenic+

#438 ACAIDI opened 4 months ago
1
'PyRanges object has no attribute', 'Count'

#437 laki-spk closed 4 months ago
1
pip installation issue

#436 swbujnowski closed 3 months ago
3
Data base

#435 SteveTur opened 4 months ago
3
how to prepare motif2tf file for `path_to_motif_annotations` in plant

#434 xuzhougeng closed 3 months ago
2
Failing to integrate scATAC + scRNA cells (non multiome data). Error in rule prepare_GEX_ACC_non_multiome:

#433 twinklevhatkar opened 4 months ago
1
TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object

#432 degrainger closed 4 months ago
3
run_cgs_models_mallet not working

#431 uqnsarke opened 4 months ago
4
Where is genome_annotation.tsv ?

#429 Zhangruiqi111 closed 4 months ago
5
A simple little question

#428 goodstudy28 opened 4 months ago
1
.raw

#427 paupaiz opened 4 months ago
0
Length mismatch when running get_search_space

#426 ytrink closed 4 months ago
4
module load cluster/wice/bigmem

#425 Zhangruiqi111 closed 4 months ago
6
Original Cells Used for pseudomultiome

#423 orian116 opened 4 months ago
1
Avoid discarding cells if one modality failed.

#421 ktroule opened 5 months ago
0
Branch missing scenicplus.cistromes modules

#418 AmosFong1 closed 4 months ago
5
ModuleNotFoundError: No module named 'scenicplus.dimensionality_reduction'

#417 dsecilmis closed 2 months ago
1
Error when overlapping scRNA-seq annotations to cistopic_obj (argmax of an empty sequence)

#416 leahyekim opened 5 months ago
6
Question: How to 'map' new SCENIC+ nomenclature with the older versions

#415 ccruizm opened 5 months ago
0
How to open pkl file generated by old scenicplus package?

#414 AIBio opened 5 months ago
5
TypeError: score_eRegulons() got an unexpected keyword argument 'scplus_obj'

#413 LukasOussoren closed 2 months ago
2
run_pycistarget is not defined

#412 DmitriiSeverinov closed 3 months ago
6
Clarification needed: Input_file for running snakemake pipieline?

#409 leahyekim closed 5 months ago
2
localrule region_to_gene

#408 TingTingShao opened 6 months ago
5
Perturbation effect issue, One sample has ~0 perturbation scores for all TFs

#405 solvi808 opened 6 months ago
0
Plots showing projection of perturbation effect in embedding look the same for all regulons

#404 solvi808 opened 6 months ago
2
it would be nice to provide the results with each step of the analysis. this would help with debugging greatly.

#402 hshcao opened 6 months ago
1
Two problems in download_genome_annotations when using old genome assemblies (with makeshift solutions)

#401 franciskim-yonsei opened 6 months ago
4
pycisTopic label transfer failure

#400 hshcao opened 6 months ago
1
can't use scenicplus command line and trouble in run_scenicplus

#399 Linshiqi-Git closed 5 months ago
0
ctx_results.hdf5 AND dem_results.hdf5, I do not understdand

#398 w1973145618 opened 6 months ago
1
installation instructions fetch outdated lda library for conda 24.4.0 & rocky-linux 8.9

#397 EmielGeeraerts opened 6 months ago
1
Passing a set as an indexer is not supported. Use a list instead.

#395 Meiyuhaha opened 6 months ago
4
Direct and extended predicted TF-to-region-to-gene links.

#394 w1973145618 closed 6 months ago
0
Problem with GRN plot

#393 SteveTur opened 6 months ago
16
Fix issue #386

#391 WhenMelancholy opened 6 months ago
0
The required file cannot be found

#390 LMBei3353 closed 6 months ago
1
Mouse GRCm38 genome is more helpful

#389 lifei176 closed 6 months ago
9
pycisTopic.iterative_peak_calling: IndexError: list index out of range

#388 hshcao closed 6 months ago
4
The tutorial for starting analysis with counting matrices cannot be opened

#387 Linshiqi-Git closed 6 months ago
1
The version of dask may need to be updated to be compatible with python 3.11.9.

#386 WhenMelancholy opened 6 months ago
3
Update docs

#385 WhenMelancholy opened 6 months ago
0
Issue installing scenicplus

#383 jkanche closed 6 months ago
3

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