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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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run_scenicplus() error before inferring TF to gene relationships
#353
jenelysRO
closed
2 months ago
5
scenicplus installation
#352
ktroule
closed
2 months ago
5
Plotting the eRegulon enrichment score using the scanpy umap function [development branch]
#351
zfliu01
closed
2 months ago
2
Linux installation Error
#350
kakaisi
opened
2 months ago
3
export_pseudobulk() does not work
#349
Ashika-Jayanthy
opened
2 months ago
2
Resource temporarily unavailable when run_scenicplus
#348
HarryShen668
closed
2 months ago
4
NameError: name 'run_cistarget' is not defined
#347
w1973145618
closed
2 months ago
3
split_fragments_by_cell_type doesn't generate proper celltype.fragments.tsv.gz file
#346
cjiang310437
closed
2 months ago
1
Issue with accessing Ensembl database via Pybiomart in tutorial
#345
HarryShen668
closed
2 months ago
0
An error related to "peak_calling"
#343
m03077yhtnt
opened
3 months ago
1
Question about installation
#342
ashleshagogate
closed
3 months ago
1
TF_cistrome_correlation
#341
hanapac
opened
3 months ago
4
Installation problem
#338
m03077yhtnt
closed
2 months ago
3
Subset regions from cistromes params and fix dotplot repressors
#337
DanieFD
opened
3 months ago
0
Installation via pip failing due to missing `master` branch in dependency
#336
henryjburg
closed
3 months ago
2
problem when run calculate_TFs_to_genes_relationships
#335
aaaaaaaaaayong
closed
3 months ago
6
No hg19 scores/dem database
#333
mwetzel7
closed
2 months ago
9
ValueError: X has 1 features, but KNeighborsClassifier is expecting 1441 features as input.
#330
nehareddies
closed
3 months ago
1
Issue with loom file export function
#329
SteveTur
opened
3 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
3 months ago
1
Empty region_to_gene_importances and region_to_gene_correlation when run_scenicplus
#325
YaoLi3
closed
3 months ago
0
Trajectory differentation arrows change each time I replot
#324
bhhlee
opened
3 months ago
0
What is the time complexity of SCENIC+?
#323
WhenMelancholy
closed
3 months ago
1
Update dockerfile please
#322
AmosFong1
closed
2 weeks ago
1
Update RSS.py
#317
SeppeDeWinter
closed
3 months ago
0
AttributeError: ('PyRanges object has no attribute', 'regionID') with create_cistopic_object_from_fragments
#316
SITRR
closed
3 months ago
2
TypeError in Branched trajectory analysis
#315
Umaarasu
closed
3 months ago
0
error for export_pseudobulk
#314
aaaaaaaaaayong
closed
3 months ago
5
create_SCENICPLUS_object(multi_ome_mode = False),Keeping 0 cells for RNA and 0 for ATAC
#313
wangdlpbr
opened
3 months ago
13
Calculate path matrices for differentiation arrows (branched tracjectory)
#312
bhhlee
opened
3 months ago
3
Generating a Umap with eRegulon AUC does not produce proper clusters
#310
redvoidling
opened
4 months ago
2
scenicplus object file request due to run_scenicplus function being extremely slow
#309
elhaam
closed
3 months ago
2
Output scenicplus
#308
SteveTur
closed
3 months ago
1
run_scenicplus Skips Steps
#304
marck1198
opened
4 months ago
0
RuntimeError from pbmc tutorial ( export_pseudobulk)
#303
Tu4n-ph4m
closed
3 months ago
10
Unable to run pbmc tutorial ( export_pseudobulk)
#302
Tu4n-ph4m
closed
4 months ago
1
run_scenicplus stops running midway
#300
peggiechien
opened
4 months ago
14
AttributeError in export_pseudobulk with Python 3.8
#299
elhaam
closed
4 months ago
2
TypeError export_pseudobulk
#298
skoturan
closed
4 months ago
3
export_pseudobulk() does not work
#297
wgao688
closed
4 months ago
34
Chromsizes URL
#296
SteveTur
opened
4 months ago
4
Mis-labelled motifs ?
#295
JaanaB1
opened
4 months ago
1
pycisTarget - TypeError: object of type 'int' has no len()
#293
simozhou
closed
5 months ago
1
'unsupported operand type' error in import export_pseudobulk
#292
cbiagii
closed
5 months ago
2
Perturbation: calculating shift along PCAs
#291
mason-sweat1
opened
5 months ago
1
MemoryError when running impute_accessibility
#290
liouhy
closed
4 months ago
4
After running GSEA. I got stuck on getting the regulons.
#288
rogercasalsfr
opened
5 months ago
4
plot Regulon different in plot_AUC_given_ax and sc.pl.umap
#287
LILI-0000-0002-8173-7367
opened
5 months ago
7
ValueError: Length mismatch: Expected axis has 0 elements, new values have 3 elements
#285
Sudheshna30
opened
5 months ago
2
RunTimeError with export_pseudobulk
#284
mairamirza
closed
5 months ago
3
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