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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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OSError: ZSTD decompression failed: Unknown frame descriptor
#97
ramadatta
opened
1 year ago
1
Update requirements + Fix tutorial bug
#95
dburkhardt
closed
1 year ago
3
Fix annotation processing - closes #93
#94
dburkhardt
closed
1 year ago
0
Genome reference improperly formatted in pmbc tutorial [BUG]
#93
dburkhardt
closed
1 year ago
0
Consider removing FA2 as a dependency as it is not actively maintained and does not pip install from PyPI on Python 3.9+
#92
dburkhardt
closed
1 year ago
1
Issue with installation
#91
sneddonucsf
closed
1 year ago
1
Attribute Error: create_SCENICPLUS_object, adata.raw.to_adata
#90
SidG13
closed
1 year ago
3
Raylet spilling error when running run_scenicplus
#89
saguilarfer
closed
1 month ago
12
issue with run_scenicplus wrapper
#88
aitortxo10
closed
1 year ago
2
issue running cistarget using human dataset
#87
sid5427
opened
1 year ago
12
peak_calling: RuntimeError No {cell_type}.bed.gz file
#86
saguilarfer
closed
1 year ago
12
ImportError
#83
klgoss
closed
1 year ago
1
Beg for human TFs motif files
#82
AIBio
closed
1 year ago
1
Pickling Scenic plus object error - 'r2g' has no attribute '_field_defaults'
#81
Sayyam-Shah
closed
1 month ago
19
cistarget - Feather V1 and V2 format - rankings and scores
#80
Sayyam-Shah
closed
1 year ago
0
Ray spill out of disk error when using run_pycistarget
#78
DavidvanBruggen
closed
1 year ago
1
AttributeError when call run_scenicplus
#76
alexwang1001
closed
1 year ago
9
Unpaired example
#75
Nusob888
closed
1 year ago
1
NaN values for DEG with scenicplus
#70
tu4n-p
closed
1 year ago
4
Tutorial 10x multiome - AssertionError: Database "{fname}" doesn't exist.
#69
Tomoya89
closed
1 year ago
7
load own filtered gene matrix and cell type annotations?
#68
sid5427
closed
1 year ago
1
Question regarding the r2g/tf2g importance scores
#67
psl-schaefer
closed
1 year ago
0
Can I use time series data with multiple replicates per time point
#66
revolvefire
closed
1 year ago
0
Question about GSEA in the eGRN compilation part
#64
tianchen2019
closed
1 year ago
0
Tutorial 10x multiome - ATAC processing
#63
JasonOSS
closed
1 year ago
8
Test data in scenicplus and pycisTopic jupyter notebook seem lost.
#62
wangmeijiao
closed
1 year ago
2
Cannot export pseudobulk files
#61
Abigail575
closed
1 year ago
3
Assertion Error running wrapper: run_pycistarget, with custom annotation
#60
SidG13
closed
1 year ago
15
Calculating correlation between gene-based regulon AUC and region-based regulon AUC
#59
liz-is
closed
1 year ago
2
run_cistarget fails when using multiple region_sets
#57
SidG13
closed
1 year ago
1
Allowing custom species for pycistarget
#56
Goultard59
closed
1 year ago
8
error for `export_pseudobulk`
#55
fengweimin-maker
closed
1 year ago
3
DAR calculation results in empty dictionary values for some keys
#53
SidG13
closed
1 year ago
3
How to speed up the "calculate_TFs_to_genes_relationships" function wrapped in "run_scenicplus"?
#52
EthanZhaoChem
closed
1 year ago
7
db_fpath and motif_annot_fpath files.
#51
sid5427
closed
1 year ago
3
Issue with scenicplus.wrappers
#50
idalarsson
closed
1 year ago
3
Dataset for 10x pbmc multiome
#49
tu4n-p
closed
1 year ago
1
How to run the run_pycistarget function locally?
#48
WhaleGe
closed
1 year ago
12
An error during calculate_TFs_to_genes_relationships()
#47
bavanesyan
closed
1 year ago
1
Add option to compute region-gene distance relative to TSS instead of gene body
#46
psl-schaefer
closed
1 year ago
4
error when running run_scenicplus
#43
longfeili5170
closed
1 year ago
7
issue with RAY package while running a jupyter notebook
#42
sid5427
closed
1 year ago
4
build_grn hanging
#41
valelorenzi9
closed
2 years ago
12
Can scRNA and scATAC paired data from multiple samples be used with Scenic+ ?
#40
WhaleGe
closed
2 years ago
1
Are SCENIC+ results stochastic?
#38
liz-is
closed
2 years ago
0
cannot find blacklist file.
#37
sid5427
closed
2 years ago
3
run_scenicplus hanging
#36
yupingz
closed
1 year ago
10
Provide files used for tutorial SCENIC+ step-by-step in the human cerebellum
#35
chrarnold
closed
2 years ago
3
Fully support sparse matrices: mismatch matrix indices in calculate_TFs_to_genes_relationships()
#34
decarlin
closed
2 years ago
3
Clarification request: what scRNA-seq data is needed to create the SCENIC+ object?
#33
liz-is
closed
2 years ago
5
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