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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Running Scenic+ without Snakemake

#510 gilgolan73 opened 3 days ago
1
Sure! Here’s the translation of your request into English: --- The **scenicplus** library is not installing. I've been trying for a month, and it doesn't install even in a Conda virtual environment. It gives the following error. Please help me to install the library. --- If you provide the specific error message you're encountering, I can assist you further in troubleshooting the installation of the **scenicplus** library.

#509 sajadfatahi closed 3 days ago
1
Sure! Here’s the translation of your request into English: --- The **scenicplus** library is not installing. I've been trying for a month, and it doesn't install even in a Conda virtual environment. It gives the following error. Please help me to install the library. --- If you provide the specific error message you're encountering, I can assist you further in troubleshooting the installation of the **scenicplus** library.

#508 sajadfatahi closed 3 days ago
1
کتابخانه scenicplus نصب نمیشه یک ماهه تلاش میکنم حتی در محیط مجازی کوندا نیز نصب نمیشه ارور زیر رو میده لطفا کری کنید بشه کتابخانه رو نصب کرد

#507 sajadfatahi opened 5 days ago
2
کتابخانه نصب نمیشه یک ماهه تلاش میکنم حتی در محیط مجازی کوندا نیز نصب نمیشه

#506 sajadfatahi opened 5 days ago
1
Unpaired examples

#503 Melody-cell closed 1 week ago
1
Can we use scenic+ with only scRNA-seq data?

#502 salihaey closed 1 week ago
1
Error in running cell_topic_heatmap

#501 realmungmung opened 2 weeks ago
0
How to run SCENIC+ with Signac processed data

#499 zhli12 opened 2 weeks ago
3
Stuck at the AUCell_direct. (insufficient memory, with 1Tb of RAM)

#498 JinKyu-Cheong opened 2 weeks ago
3
Plotting a network

#495 sugiYag opened 3 weeks ago
3
secnicpluts run error

#494 sugiYag closed 3 weeks ago
0
InvalidIndexError: (slice(None, None, None), 30751) while using coverage plot

#493 yojetsharma opened 3 weeks ago
2
Error in rule get_search_space: jobid: 11 second

#492 vcleon88 opened 4 weeks ago
2
Error in rule get_search_space: jobid: 11

#491 vcleon88 opened 4 weeks ago
1
ValueError: Length mismatch: Expected axis has 0 elements, new values have 3 elements

#490 JinKyu-Cheong closed 4 weeks ago
0
[API question] what is the difference between scplus_obj from "running scenic+ documentation" vs "created using GEX.h5ad+cistopic_obj in API"?

#489 yojetsharma closed 3 weeks ago
0
What's the meaning of the suffix of output eregulon's name like "+/+" or "+/-" ?

#488 XinWang19 closed 1 week ago
1
plot_rss problem

#487 GGboy-Zzz opened 1 month ago
1
Missing Expected Outputs in SCENIC+ Pipeline

#486 yojetsharma closed 3 weeks ago
1
export_pseudobulk Error append after pseudobulk_bed_files output produced

#485 zhenghuiwen-bgi closed 1 month ago
4
adata.raw overwritten with normalized counts in SCENIC+ pipeline

#484 cjiang310437 opened 1 month ago
1
SCENIC+ build fails due to annoy package

#483 mairamirza closed 1 month ago
2
Chromsize file issue, snakemake doesn't proceed

#482 yojetsharma closed 1 month ago
5
Error in running grn_inference region_to_gene

#481 Longity opened 1 month ago
1
conda.sh file question

#480 sugiYag closed 1 month ago
0
SCENIC+ fails to install due to pybigtools build failure

#479 dmalzl opened 1 month ago
7
Alternative to bigmem?

#477 yojetsharma closed 1 month ago
2
Error in download_genome_annotations: "Could not find IdList" / "Could not find DocSum"

#476 kennethho04 closed 1 month ago
4
Issue with pycisTopic on human cerebellum single-cell multiome data on HPC Fedora

#475 Stack7 opened 1 month ago
2
Problem with TSS

#474 ReviewBrandLab2024 opened 1 month ago
3
scenicplus prepare_data prepare_menr error

#470 Yiming-Huang-neuron opened 2 months ago
6
Understanding scenicPlus settings and Outputs

#469 orian116 closed 1 month ago
0
Error when running SnakeMake

#468 gilgolan73 opened 2 months ago
19
Problems with importing for new, Tutorial: Perturbation simulation

#467 finncreeggan opened 2 months ago
1
Re-calculating enrichment scores after filtering eRegulons and "+"/ "-" eRegulon signs

#466 maithermbarros opened 2 months ago
5
create_cistopic_object_from_fragments run forever

#465 Quentin-bioinfo closed 2 months ago
0
Creating custom cistarget database

#462 zznx opened 2 months ago
0
Issue while Installing on Fedora HPC Using conda environment

#461 Stack7 opened 2 months ago
3
Error in rule eGRN_extended - ValueError: No objects to concatenate

#460 maithermbarros closed 2 months ago
2
Pycistopic Temporary Fragment file cannot be found

#458 yrsong001 opened 2 months ago
1
Re-running old SCENIC+ pipeline in the new version without snakemake

#457 skoturan closed 2 months ago
2
Update perturbation simulation

#456 SeppeDeWinter closed 2 months ago
0
SCENIC+ crashed in tf_to_gene step

#454 kangjiajinlong opened 2 months ago
3
how much resource needed? Multiome datasets with 270k cells

#453 JinKyu-Cheong closed 3 months ago
1
Input annotated 10x Multiome Seurat object into SCENIC+

#452 strawberry098 closed 3 months ago
1
Region set, scores.feather and NameError: name 'run_cgs_models_mallet

#451 strawberry098 opened 3 months ago
3
QC files are not formed

#450 gilgolan73 closed 2 months ago
5
`ValueError: No objects to concatenate` during `motif_enrichment_dem` Execution

#449 OjongTabi opened 3 months ago
2
How can I convert a SCENIC+ object to a loom file?

#448 uqnsarke opened 3 months ago
0