aertslab/pySCENIC issues and pull requests

#472 - Arboreto with multiprocessing script seemingly taking too long

Issue - State: open - Opened by wbrett87 over 1 year ago - 1 comment

#471 - Singularity container fails: "ModuleNotFoundError: No module named 'pandas.io.formats.csvs'"

Issue - State: closed - Opened by tilofrei over 1 year ago - 3 comments
Labels: bug

#470 - Error report: pyscenic aucell

Issue - State: closed - Opened by ojikj2019 over 1 year ago - 9 comments
Labels: bug

#469 - [results] How to get Regulon - Target - Importance file?

Issue - State: open - Opened by bvaldebenitom over 1 year ago
Labels: question

#468 - pyarrow.lib.ArrowInvalid: Not a feather file

Issue - State: open - Opened by qiruicheng over 1 year ago - 4 comments
Labels: bug

#467 - [BUG]what is signatures_fname required by aucell?

Issue - State: open - Opened by caodudu over 1 year ago - 3 comments
Labels: bug

#466 - pyscenic warning: less than 80% of the genes in xxx could be mapped to ...

Issue - State: open - Opened by Beki-seq over 1 year ago - 2 comments
Labels: bug

#465 - Correcting the "CLI ctx fails on 'dask_cluster' mode" bug

Pull Request - State: closed - Opened by carlos-a-enriquez over 1 year ago - 1 comment

#464 - Correcting the "CLI ctx fails on 'dask_cluster' mode" bug

Pull Request - State: closed - Opened by carlos-a-enriquez over 1 year ago - 1 comment

#463 - arboreto_with_multiprocessing.py not able to use specified threads

Issue - State: open - Opened by MarcusLCC over 1 year ago - 6 comments
Labels: bug

#462 - CLI ctx fails on "dask_cluster" mode[BUG]

Issue - State: closed - Opened by carlos-a-enriquez over 1 year ago - 1 comment
Labels: bug

#461 - Bug Modules for iRegulons

Issue - State: open - Opened by StevenTur over 1 year ago
Labels: bug

#460 - f_db_names outputs empty

Issue - State: open - Opened by Jiayi-Zheng over 1 year ago - 1 comment
Labels: bug

#459 - [BUG]pyscenic aucell generated totally same loom file as the input loom, but can be correct if "csv"

Issue - State: open - Opened by KOBE24DUNK over 1 year ago - 2 comments
Labels: bug

#458 - AttributeError: module 'scanpy' has no attribute 'utils'

Issue - State: open - Opened by yanwuanxin almost 2 years ago - 1 comment
Labels: bug

#457 - [BUG] Human transcription factors list

Issue - State: open - Opened by malosreet almost 2 years ago - 2 comments
Labels: bug

#456 - Cancelled and Closed

Issue - State: closed - Opened by KOBE24DUNK almost 2 years ago
Labels: bug

#455 - [Closed]It would be better if pyscenic can save temporary files like it in R.

Issue - State: closed - Opened by KOBE24DUNK almost 2 years ago
Labels: bug

#454 - prune2df report error

Issue - State: open - Opened by zzzseeu almost 2 years ago - 2 comments
Labels: bug

#453 - Error in picking out modules for iRegulon: print( f'{tf} regulon: {len(regulons[tf])} genes' ) KeyError: 'TF name'

Issue - State: open - Opened by stanaka6 almost 2 years ago - 1 comment
Labels: bug

#452 - pyscenic ctx terminates: pyarrow.lib.ArrowInvalid: Not a feather file

Issue - State: closed - Opened by northNomad almost 2 years ago - 1 comment
Labels: bug

#451 - Please delete it, because problem was solved automatically

Issue - State: closed - Opened by KOBE24DUNK almost 2 years ago
Labels: bug

#450 - Cancelled and Closed

Issue - State: closed - Opened by KOBE24DUNK almost 2 years ago
Labels: bug

#449 - [question] Getting additional positive regulons on enabling --all_modules option in pySCENIC

Issue - State: open - Opened by nitinnarwade almost 2 years ago - 2 comments
Labels: question

#448 - [results]

Issue - State: open - Opened by JensFGG almost 2 years ago
Labels: question

#447 - Running error of pyscenic aucell[ERROR]

Issue - State: closed - Opened by Xicici-Yan almost 2 years ago
Labels: bug

#446 - Problem cancelled.

Issue - State: closed - Opened by KOBE24DUNK almost 2 years ago

#445 - Nextflow PYSCENIC DSL2 stops running after the first two first two steps

Issue - State: open - Opened by mt98 almost 2 years ago - 2 comments

#444 - filter processig error using nextflow

Issue - State: closed - Opened by Erfan1369 almost 2 years ago
Labels: question

#443 - [BUG]AttributeError: 'numpy.ndarray' object has no attribute 'split

Issue - State: open - Opened by Sa753 almost 2 years ago - 1 comment
Labels: bug

#442 - Error in grn (about tornado.application)[BUG] [BUG]

Issue - State: open - Opened by Sa753 almost 2 years ago - 2 comments
Labels: bug

#441 - BrokenPipeError: [WinError 109][BUG]

Issue - State: open - Opened by Su870 about 2 years ago - 2 comments
Labels: bug

#440 - [BUG]running the "Full pipeline.ipynb"

Issue - State: open - Opened by CCCKW about 2 years ago - 1 comment
Labels: bug

#439 - [BUG]from pyscenic.rnkdb import FeatherRankingDatabase as RankingDatabase

Issue - State: open - Opened by CCCKW about 2 years ago - 5 comments
Labels: bug

#438 - [BUG] Error opening output loom file

Issue - State: open - Opened by Prathyusha-konda about 2 years ago - 2 comments
Labels: bug

#437 - Issue Generating Pyscenic GRN adj.csv file

Issue - State: open - Opened by Su870 about 2 years ago - 2 comments

#436 - [ERROR] GRN step quits with

Issue - State: closed - Opened by ishwarvh about 2 years ago - 2 comments
Labels: bug

#435 - Error running example PBMC data using nextflow

Issue - State: open - Opened by bapoorva about 2 years ago - 4 comments

#434 - Pyscenic running grn multiple times

Issue - State: open - Opened by LinearParadox about 2 years ago - 3 comments
Labels: bug

#433 - Transcription factor database sources[results]

Issue - State: closed - Opened by fangshansh about 2 years ago - 1 comment
Labels: question

#432 - [BUG] ctx step hangs at "Writing to file" step

Issue - State: closed - Opened by twoneu about 2 years ago - 2 comments
Labels: bug

#431 - Fatal error condition occurred in event_loop.c:72: aws_thread_launch

Issue - State: open - Opened by cchen22 about 2 years ago - 3 comments
Labels: bug

#430 - Clustering

Issue - State: closed - Opened by Erfan1369 about 2 years ago - 2 comments
Labels: question

#429 - [BUG] Not clearing memory after arboreto_with_multiprocessing.py

Issue - State: closed - Opened by JensFGG about 2 years ago - 2 comments
Labels: bug

#428 - What's the meaning of the index in the *genes_vs_motifs.ranking.feather

Issue - State: closed - Opened by shangguandong1996 about 2 years ago - 1 comment
Labels: question

#427 - "could not convert string to float: " error when running cisTarget

Issue - State: open - Opened by mchua4 about 2 years ago - 1 comment

#426 - GRN on Large Dataset - 999 GB and 16 cores

Issue - State: open - Opened by Sayyam-Shah about 2 years ago - 6 comments

#425 - pyscenic ctx gives a TypeError: BaseProcess._bootstrap() takes 1 positional argument but 2 were given and an EOFError

Issue - State: closed - Opened by JewelBanik about 2 years ago - 5 comments
Labels: bug

#424 - Pyscenic vs scenic GENIE3[results]

Issue - State: closed - Opened by JensFGG about 2 years ago - 2 comments
Labels: question

#423 - CTX process gets killed

Issue - State: closed - Opened by JensFGG about 2 years ago - 4 comments

#422 - zero-score regulon

Issue - State: closed - Opened by wangjiawen2013 about 2 years ago - 3 comments
Labels: results

#421 - 'gene_names' is not defined ERROR running arboreto_with_multiprocessing.py

Issue - State: open - Opened by lindaseong about 2 years ago - 6 comments

#420 - [BUG]“pyscenic ctx” cant not load “.feather” correctly

Issue - State: open - Opened by JRZL123 about 2 years ago - 7 comments
Labels: bug

#419 - Bug using motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl file[BUG]

Issue - State: closed - Opened by Famingzhao over 2 years ago - 1 comment
Labels: bug

#418 - Error in grn (about tornado.application)[BUG]

Issue - State: closed - Opened by mengfeiwangdmu over 2 years ago - 5 comments
Labels: bug

#417 - Error: Unable to allocate 3.11 GiB for an array with shape (17627, 23657) and data type float64

Issue - State: closed - Opened by Erfan1369 over 2 years ago - 8 comments
Labels: bug

#416 - a question about parallel computing [results]

Issue - State: open - Opened by Shiywa over 2 years ago - 6 comments
Labels: question

#415 - How to install an older version of pyscenic

Issue - State: open - Opened by chentongouc over 2 years ago - 2 comments
Labels: bug

#414 - Error on running AUCELL

Issue - State: closed - Opened by Erfan1369 over 2 years ago
Labels: bug

#413 - the motif annotation databases for the new 0.12.0 release

Issue - State: open - Opened by deevdevil88 over 2 years ago - 4 comments
Labels: question

#412 - Bump nbconvert from 6.0.7 to 6.3.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#411 - Bump mistune from 0.8.4 to 2.0.3

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#410 - Fail to download resources

Issue - State: closed - Opened by FionaMoon over 2 years ago - 2 comments
Labels: question

#409 - GRN step

Issue - State: open - Opened by Sayyam-Shah over 2 years ago - 4 comments
Labels: question

#408 - cisTarget problem on the FeatherRankingDatabase command

Issue - State: open - Opened by farhad-zare over 2 years ago - 5 comments
Labels: question

#405 - [BUG] an error in pySCENIC grnboost2 in Jupyder

Issue - State: open - Opened by socialtree-yt over 2 years ago - 1 comment
Labels: bug

#404 - Bump distributed from 2021.2.0 to 2021.10.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#403 - Pyscenic ctx Feather Error

Issue - State: closed - Opened by Sayyam-Shah over 2 years ago - 7 comments
Labels: question

#402 - grnboost2 limit

Issue - State: open - Opened by wangjiawen2013 over 2 years ago - 3 comments
Labels: question

#401 - Bump numpy from 1.20.1 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#399 - NES and p-value

Issue - State: open - Opened by wangjiawen2013 over 2 years ago - 1 comment
Labels: question

#398 - grnboost2 limit

Issue - State: closed - Opened by wangjiawen2013 over 2 years ago - 1 comment
Labels: duplicate, question

#397 - [strategy]

Issue - State: open - Opened by BanafshehKhaki over 2 years ago - 1 comment
Labels: question

#395 - [BUG] Error in running pyscenic through docker image

Issue - State: open - Opened by thereallda over 2 years ago - 2 comments
Labels: bug

#394 - OSError: Unable to open file (message not aligned)

Issue - State: open - Opened by Li-mengjie over 2 years ago - 1 comment
Labels: bug

#392 - Want to convert h5ad file to .h5seurat

Issue - State: open - Opened by seemak21 over 2 years ago - 1 comment

#388 - singularity pyscenic grn raises segmentation fault [BUG]

Issue - State: open - Opened by biostu24 over 2 years ago - 3 comments
Labels: bug

#380 - How to use module file created by pyscenic in iRegulon?

Issue - State: open - Opened by youwh1996 over 3 years ago - 3 comments
Labels: python

#378 - Errors with running pySCENIC in conda environment or through docker/singularity images

Issue - State: open - Opened by fouerghi over 3 years ago - 4 comments
Labels: python

#377 - Missing TFs in resources

Issue - State: open - Opened by nasjr08 over 2 years ago - 9 comments

#374 - How to choose the ranking database

Issue - State: closed - Opened by Tianran1 over 2 years ago - 2 comments
Labels: results

#373 - Bump pillow from 8.1.1 to 9.0.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#371 - Installation error with python 3.9[BUG]

Issue - State: open - Opened by frenkiboy over 2 years ago - 5 comments
Labels: bug

#365 - [results] prepare loom file for SCope - HOWTO

Issue - State: closed - Opened by wariobrega almost 3 years ago - 4 comments
Labels: results

#361 - Bump ipython from 7.20.0 to 7.31.1

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#352 - pbmc10k_scenic_integrated-output.loom cannot be loaded

Issue - State: closed - Opened by hyjforesight almost 3 years ago - 8 comments
Labels: bug

#350 - AttributeError: 'numpy.ndarray' object has no attribute 'quantile' when doing nGenesDetectedPerCell.quantile()

Issue - State: closed - Opened by hyjforesight almost 3 years ago - 8 comments
Labels: bug

#338 - Bump dask from 2021.2.0 to 2021.10.0

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#335 - [BUG] pyscenic grn crashes with: Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.

Issue - State: closed - Opened by mcsimenc about 3 years ago - 2 comments
Labels: bug

GitHub / aertslab/pySCENIC issues and pull requests