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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KeyError: 'Gene' in get_search_space

#381 orian116 opened 6 months ago
11
Parameters of scenicplus

#380 XiaoKaixuan12333 closed 6 months ago
0
Issue with can't find the original scenicplus tutorial documentation

#379 LMBei3353 closed 6 months ago
2
No enriched motifs found in Topics/DAR

#377 XiaoKaixuan12333 closed 6 months ago
2
Incorrect preparation of non-multiome data causes error in the step 'Calculating region to gene importance, using GMB method'

#376 AthanasiaSt closed 6 months ago
1
Error when running run_cgs_model_mallet

#375 EddieLv closed 6 months ago
0
Length mismatch: Expected axis has 0 elements, new values have 3 elements

#374 XiaoKaixuan12333 closed 6 months ago
1
multi_ome_mode = False

#372 orian116 closed 6 months ago
3
Trouble with run_pycistarget

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

#369 aaaaaaaaaayong closed 6 months ago
3
ModuleNotFoundError: No module named 'pyranges.pyranges_main'

#368 janursa opened 7 months ago
10
Error in 'process_non_multiome_data' - imputed_acc_obj.feature_names contains regions not present in ACC_region_metadata

#367 jesswhitts opened 7 months ago
6
Step by step pipeline

#366 SteveTur closed 6 months ago
4
UnicodeEncodeError: 'ascii' codec can't encode character '\u2013' in position 21: ordinal not in range(128)

#364 DmitriiSeverinov closed 6 months ago
3
Error building pybigtools while installing SCENIC+

#363 TemiLeke closed 7 months ago
0
export_pseudobulk error: fragment file does not exist

#360 TemiLeke closed 7 months ago
1
Interoperability between mudata and scplus obj

#358 jesswhitts closed 7 months ago
4
Snakemake pipeline stalls on 'download_genome_annotations'

#357 jesswhitts opened 7 months ago
3
None of [Index([dtype='object', length=)] are in the [columns] Scenicplus snakemake cistopic object

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

#354 Daliya-K closed 7 months ago
3
run_scenicplus() error before inferring TF to gene relationships

#353 jenelysRO closed 7 months ago
5
scenicplus installation

#352 ktroule closed 7 months ago
5
Plotting the eRegulon enrichment score using the scanpy umap function [development branch]

#351 zfliu01 closed 7 months ago
2
Linux installation Error

#350 kakaisi opened 7 months ago
3
export_pseudobulk() does not work

#349 Ashika-Jayanthy opened 7 months ago
2
Resource temporarily unavailable when run_scenicplus

#348 HarryShen668 closed 7 months ago
4
NameError: name 'run_cistarget' is not defined

#347 w1973145618 closed 7 months ago
3
split_fragments_by_cell_type doesn't generate proper celltype.fragments.tsv.gz file

#346 cjiang310437 closed 7 months ago
1
Issue with accessing Ensembl database via Pybiomart in tutorial

#345 HarryShen668 closed 7 months ago
0
An error related to "peak_calling"

#343 m03077yhtnt opened 7 months ago
5
Question about installation

#342 ashleshagogate closed 7 months ago
1
TF_cistrome_correlation

#341 hanapac opened 7 months ago
4
Installation problem

#338 m03077yhtnt closed 7 months ago
3
Subset regions from cistromes params and fix dotplot repressors

#337 DanieFD opened 8 months ago
0
Installation via pip failing due to missing `master` branch in dependency

#336 henryjburg closed 8 months ago
2
problem when run calculate_TFs_to_genes_relationships

#335 aaaaaaaaaayong closed 7 months ago
6
No hg19 scores/dem database

#333 mwetzel7 closed 7 months ago
9
ValueError: X has 1 features, but KNeighborsClassifier is expecting 1441 features as input.

#330 nehareddies closed 8 months ago
1
Issue with loom file export function

#329 SteveTur opened 8 months ago
5
hg38_screen_v10_clust.regions_vs_motifs.rankings.feather" is not a cisTarget Feather database in Feather v1 or v2 format

#328 SITRR closed 8 months ago
1
Empty region_to_gene_importances and region_to_gene_correlation when run_scenicplus

#325 YaoLi3 closed 8 months ago
0
Trajectory differentation arrows change each time I replot

#324 bhhlee opened 8 months ago
0
What is the time complexity of SCENIC+?

#323 WhenMelancholy closed 8 months ago
1
Update dockerfile please

#322 AmosFong1 closed 5 months ago
1
Update RSS.py

#317 SeppeDeWinter closed 8 months ago
0
AttributeError: ('PyRanges object has no attribute', 'regionID') with create_cistopic_object_from_fragments

#316 SITRR closed 8 months ago
2
TypeError in Branched trajectory analysis

#315 Umaarasu closed 8 months ago
0
error for export_pseudobulk

#314 aaaaaaaaaayong closed 8 months ago
6
create_SCENICPLUS_object(multi_ome_mode = False),Keeping 0 cells for RNA and 0 for ATAC

#313 wangdlpbr opened 8 months ago
14
Calculate path matrices for differentiation arrows (branched tracjectory)

#312 bhhlee opened 8 months ago
3

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