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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Avoid discarding cells if one modality failed.

#421 ktroule opened 1 week ago
0
Branch missing scenicplus.cistromes modules

#418 AmosFong1 opened 2 weeks ago
3
ModuleNotFoundError: No module named 'scenicplus.dimensionality_reduction'

#417 dsecilmis opened 2 weeks ago
0
Error when overlapping scRNA-seq annotations to cistopic_obj (argmax of an empty sequence)

#416 leahyekim opened 2 weeks ago
2
Question: How to 'map' new SCENIC+ nomenclature with the older versions

#415 ccruizm opened 2 weeks ago
0
How to open pkl file generated by old scenicplus package?

#414 AIBio opened 2 weeks ago
3
TypeError: score_eRegulons() got an unexpected keyword argument 'scplus_obj'

#413 LukasOussoren opened 3 weeks ago
1
run_pycistarget is not defined

#412 DmitriiSeverinov opened 3 weeks ago
1
Clarification needed: Input_file for running snakemake pipieline?

#409 leahyekim closed 3 weeks ago
2
localrule region_to_gene

#408 TingTingShao opened 1 month ago
5
Perturbation effect issue, One sample has ~0 perturbation scores for all TFs

#405 solvi808 opened 1 month ago
0
Plots showing projection of perturbation effect in embedding look the same for all regulons

#404 solvi808 opened 1 month 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 1 month ago
1
Two problems in download_genome_annotations when using old genome assemblies (with makeshift solutions)

#401 franciskim-yonsei opened 1 month ago
3
pycisTopic label transfer failure

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

#399 Linshiqi-Git closed 3 weeks ago
0
ctx_results.hdf5 AND dem_results.hdf5, I do not understdand

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installation instructions fetch outdated lda library for conda 24.4.0 & rocky-linux 8.9

#397 EmielGeeraerts opened 1 month ago
0
Passing a set as an indexer is not supported. Use a list instead.

#395 Meiyuhaha opened 1 month ago
3
Direct and extended predicted TF-to-region-to-gene links.

#394 w1973145618 closed 1 month ago
0
Problem with GRN plot

#393 SteveTur opened 1 month ago
6
Fix issue #386

#391 WhenMelancholy opened 1 month ago
0
The required file cannot be found

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

#389 lifei176 closed 1 month ago
2
pycisTopic.iterative_peak_calling: IndexError: list index out of range

#388 hshcao closed 1 month ago
4
The tutorial for starting analysis with counting matrices cannot be opened

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

#386 WhenMelancholy opened 1 month ago
1
Update docs

#385 WhenMelancholy opened 1 month ago
0
Issue installing scenicplus

#383 jkanche closed 1 month ago
3
KeyError: 'Gene' in get_search_space

#381 orian116 opened 1 month ago
11
Parameters of scenicplus

#380 XiaoKaixuan12333 closed 1 month ago
0
Issue with can't find the original scenicplus tutorial documentation

#379 LMBei3353 closed 1 month ago
2
No enriched motifs found in Topics/DAR

#377 XiaoKaixuan12333 closed 1 month ago
2
Incorrect preparation of non-multiome data causes error in the step 'Calculating region to gene importance, using GMB method'

#376 AthanasiaSt closed 1 month ago
1
Error when running run_cgs_model_mallet

#375 EddieLv closed 1 month ago
0
Length mismatch: Expected axis has 0 elements, new values have 3 elements

#374 XiaoKaixuan12333 closed 1 month ago
1
multi_ome_mode = False

#372 orian116 closed 1 month ago
3
Trouble with run_pycistarget

#370 mwetzel7 opened 2 months ago
7
some questions about the function score_eRegulons

#369 aaaaaaaaaayong closed 1 month ago
2
ModuleNotFoundError: No module named 'pyranges.pyranges_main'

#368 janursa opened 2 months ago
9
Error in 'process_non_multiome_data' - imputed_acc_obj.feature_names contains regions not present in ACC_region_metadata

#367 jesswhitts opened 2 months ago
5
Step by step pipeline

#366 SteveTur closed 1 month ago
4
UnicodeEncodeError: 'ascii' codec can't encode character '\u2013' in position 21: ordinal not in range(128)

#364 DmitriiSeverinov closed 1 month ago
3
Error building pybigtools while installing SCENIC+

#363 TemiLeke closed 2 months ago
0
export_pseudobulk error: fragment file does not exist

#360 TemiLeke closed 2 months ago
1
Interoperability between mudata and scplus obj

#358 jesswhitts closed 2 months ago
4
Snakemake pipeline stalls on 'download_genome_annotations'

#357 jesswhitts opened 2 months ago
1
None of [Index([dtype='object', length=)] are in the [columns] Scenicplus snakemake cistopic object

#355 Baudicm closed 2 months ago
7
Installation issue (scenicplus and pyscenic conflicting dependencies)

#354 Daliya-K closed 2 months ago
3
run_scenicplus() error before inferring TF to gene relationships

#353 jenelysRO closed 2 months ago
5