Ecosyste.ms: Issues

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GitHub / aertslab/pySCENIC issues and pull requests

#578 - ERROR: module 'numpy' has no attribute 'object'

Issue - State: open - Opened by xyang2uchicago 2 months ago - 1 comment
Labels: bug

#576 - getAUC fucntion error

Issue - State: open - Opened by apal6 2 months ago
Labels: bug

#575 - binarize function error

Issue - State: open - Opened by apal6 2 months ago
Labels: bug

#574 - Database creation for Killifish

Issue - State: open - Opened by juhi-ku 3 months ago

#573 - Correct TF File

Issue - State: open - Opened by amiramarouf 3 months ago
Labels: question

#572 - pyscenic aucell

Issue - State: closed - Opened by zznx 3 months ago - 2 comments
Labels: bug

#571 - Time pyscenic grn step in conda versus image

Issue - State: closed - Opened by Sirin24 3 months ago

#570 - compare between different conditions

Issue - State: open - Opened by Sirin24 3 months ago

#569 - Different batches/studies

Issue - State: open - Opened by Flu09 3 months ago - 2 comments

#568 - how to generate the heat map plot of the modules ?

Issue - State: open - Opened by Flu09 3 months ago - 1 comment
Labels: question

#567 - [BUG] pyscenic grn and type error

Issue - State: open - Opened by tutu256 3 months ago - 1 comment
Labels: bug

#566 - IDs for TFs missing

Issue - State: open - Opened by chrarnold 4 months ago - 1 comment
Labels: bug

#565 - [BUG] typeerro when import scanpy with pyscenic in conda

Issue - State: closed - Opened by Quentin-bioinfo 4 months ago - 6 comments
Labels: bug

#563 - [BUG] empty adjacencies file when running pyscenic grn via docker

Issue - State: open - Opened by iammrtza 4 months ago - 1 comment
Labels: bug

#561 - [BUG] grnboost2 TypeError: Must supply at least one delayed object

Issue - State: open - Opened by AAA-3 4 months ago - 4 comments
Labels: bug

#560 - [BUG]pyscenic grn ERR when running on HPC with slurm

Issue - State: open - Opened by jung233 4 months ago - 1 comment
Labels: bug

#559 - [BUG] run in pyscenic grn

Issue - State: open - Opened by zhangdong360 5 months ago - 8 comments
Labels: bug

#558 - ERROR - Error in Nanny killing Worker subprocess

Issue - State: closed - Opened by ASNbioinf 5 months ago - 1 comment
Labels: bug

#557 - [ERROR] in running Pyscenic GRN grnboost2

Issue - State: open - Opened by husain223 5 months ago - 2 comments
Labels: bug

#555 - ctx pyscenic Error

Issue - State: open - Opened by angelica-varesi 5 months ago - 1 comment
Labels: bug

#554 - TypeError("Must supply at least one delayed object")

Issue - State: open - Opened by lpalvin 5 months ago - 4 comments
Labels: bug

#553 - Expression matrix should be provided in the loom file format.[BUG]

Issue - State: open - Opened by bitcometz 6 months ago - 3 comments
Labels: bug

#551 - prune2df fails with TypeError: object of type 'generator' has no len() [BUG]

Issue - State: open - Opened by dmalzl 6 months ago - 2 comments
Labels: bug

#550 - [question] Can use `xgboost` or `lightgbm`

Issue - State: open - Opened by Liripo 6 months ago - 1 comment
Labels: question

#548 - [feature request] modules_from_adjacencies don't support csr matrix

Issue - State: closed - Opened by Liripo 6 months ago
Labels: bug

#547 - CTX running infinitely long. Defunct child processes

Issue - State: closed - Opened by arunchakra 6 months ago - 1 comment
Labels: bug

#546 - Can pySCENIC only run on Linux? Is it possible to use it on Windows?

Issue - State: open - Opened by Always-Stude 6 months ago - 2 comments
Labels: bug

#545 - [results]There is no X_pca? obsm: 'X_umap', 'X_tsne'

Issue - State: open - Opened by yllahmu 7 months ago - 1 comment
Labels: question

#544 - [results] different input files or loom versions having different auccell loom results

Issue - State: open - Opened by lexuziandyu 7 months ago - 1 comment
Labels: question

#543 - [BUG] AttributeError: module 'numpy' has no attribute 'float'.

Issue - State: open - Opened by juniajvs 7 months ago - 5 comments
Labels: bug

#542 - Regulon Specificity Scores Are Correlated With Size

Issue - State: closed - Opened by ggruenhagen3 7 months ago - 2 comments
Labels: bug

#541 - [question] hg19 tf list

Issue - State: open - Opened by colin893 7 months ago - 1 comment
Labels: bug

#539 - [BUG] A new bug of pysenic grn function

Issue - State: closed - Opened by HelloWorldLTY 7 months ago - 3 comments
Labels: bug

#538 - Is pyscenic grn proceeding? It does not throw any responses.

Issue - State: open - Opened by hansong798 8 months ago - 4 comments
Labels: question

#537 - [results]Transcription factor activity from AUCell result

Issue - State: open - Opened by QianLLLL 8 months ago
Labels: question

#536 - [BUG] Numpy Object Deprecation Error

Issue - State: closed - Opened by Tripfantasy 8 months ago - 5 comments
Labels: bug

#530 - [BUG]exceeded distributed.worker_memory

Issue - State: open - Opened by xgqyoung 9 months ago - 2 comments
Labels: bug

#529 - [BUG] Empty adjacent.tsv file generated: troubleshooting pyscenic grn analysis via Docker

Issue - State: closed - Opened by amberqiong 9 months ago - 6 comments
Labels: bug

#528 - [BUG] early termination of pyscenic ctx with no error message

Issue - State: open - Opened by Mira0507 10 months ago - 3 comments
Labels: bug

#525 - Error running GRNBoost2 step

Issue - State: open - Opened by eblchen 10 months ago - 18 comments

#524 - large dataset failed

Issue - State: open - Opened by wangjiawen2013 11 months ago - 1 comment
Labels: bug

#523 - Scenic is not compatible with snakemake

Issue - State: open - Opened by wangjiawen2013 11 months ago - 6 comments
Labels: bug

#522 - [BUG]not shutting down client, client was created externally

Issue - State: open - Opened by asmlgkj 11 months ago - 2 comments
Labels: bug

#521 - add_scenic_metadata error[BUG]

Issue - State: closed - Opened by AnjaliS1 12 months ago
Labels: bug

#520 - auc bug

Issue - State: open - Opened by AnjaliS1 12 months ago - 1 comment
Labels: bug

#519 - how to merge loom file of per celltype and to visualize？

Issue - State: open - Opened by Jingle0814 12 months ago
Labels: question

#518 - [BUG] Installation error

Issue - State: open - Opened by as7a5 12 months ago - 3 comments
Labels: bug

#517 - PyScenic ctx output (AUC values) [results]

Issue - State: open - Opened by stefanerb89 12 months ago
Labels: question

#516 - [results] Question about pySCENIC result

Issue - State: open - Opened by watermelontreesjs 12 months ago
Labels: question

#515 - [BUG] pyscenic.transform warning/error

Issue - State: open - Opened by stefanerb89 12 months ago - 1 comment
Labels: bug

#511 - Similare Transcription factor in TF resources

Issue - State: open - Opened by Erfan1369 about 1 year ago - 1 comment
Labels: question

#510 - pyscenic aucell command does not complete

Issue - State: open - Opened by leeanapeters about 1 year ago - 1 comment
Labels: bug

#509 - df2regulons splitting gene names by character

Issue - State: closed - Opened by Tripfantasy about 1 year ago - 1 comment

#507 - [BUG] grn stuck on "Inferring regulatory networks" when CLI ran as slurm script

Issue - State: closed - Opened by Tripfantasy about 1 year ago - 1 comment
Labels: bug

#506 - [BUG]pyscenic ctx --no_pruning

Issue - State: open - Opened by ken-chen-18 about 1 year ago
Labels: bug

#505 - [BUG] unexpected changing of data type in dataframe

Issue - State: open - Opened by whoisleehom about 1 year ago - 5 comments
Labels: bug

#504 - [BUG] pyscenic grn

Issue - State: open - Opened by ken-chen-18 about 1 year ago - 1 comment
Labels: bug

#502 - OverflowError: cannot serialize a bytes object larger than 4 GiB[Error]

Issue - State: open - Opened by liliyuan001 about 1 year ago
Labels: bug

#501 - How to use SCENIC analysis of yeast?

Issue - State: open - Opened by tuqiang2014 about 1 year ago
Labels: question

#499 - [BUG]

Issue - State: closed - Opened by fizwit over 1 year ago - 2 comments
Labels: bug

#497 - [BUG] Don't know what's wrong

Issue - State: open - Opened by yixxx091 over 1 year ago - 1 comment
Labels: bug

#496 - Usage cannot be printed after successful installation of pySCENIC

Issue - State: open - Opened by YangLi-Bio over 1 year ago - 1 comment
Labels: bug

#495 - add Dockerfile.macos for Macos user(Arm arch m1 chip etc...)

Pull Request - State: open - Opened by MGMCN over 1 year ago - 2 comments

#494 - The docker image should support the macos arm architecture.

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

#493 - prune2df empty

Issue - State: open - Opened by GeneVector5 over 1 year ago
Labels: bug

#492 - msgpack.exceptions.ExtraData: unpack(b) received extra data.

Issue - State: open - Opened by GeneVector5 over 1 year ago - 1 comment
Labels: bug

#491 - download https://resources.aertslab.org/cistarget/

Issue - State: open - Opened by GeneVector5 over 1 year ago
Labels: bug

#490 - Questions about AUCell's results

Issue - State: open - Opened by qijt123 over 1 year ago - 1 comment
Labels: question

#489 - Error when running pyscenic aucell.

Issue - State: closed - Opened by Dingpw over 1 year ago - 1 comment
Labels: bug

#488 - when use the nextflow pipeline, get a error:pyarrow.lib.ArrowInvalid: Not a feather file

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

#487 - [ERROR]

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

#486 - Input of cisTarget databases

Issue - State: open - Opened by Shin8a over 1 year ago - 3 comments
Labels: question

#485 - [BUG] grn problem about running long jobs on HPC using scheduled manager "SLURM"

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

#484 - OverflowError: cannot serialize a bytes object larger than 4 GiB

Issue - State: closed - Opened by ShuaiChen4136 over 1 year ago - 2 comments
Labels: bug

#483 - prune2df TypeError: Columns must be indices or names.

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

#482 - distributed.worker - WARNING - Could not find data:

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

#481 - [BUG]

Issue - State: open - Opened by xujie1020 over 1 year ago - 3 comments
Labels: bug

#480 - [BUG]pyscenic ctx question！

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

#479 - duplicate 'row.names' are not allowed

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

#478 - Pin numpy until np.object is not used anymore

Pull Request - State: open - Opened by pcm32 over 1 year ago - 4 comments

#477 - [BUG] New installs of PySCENIC will fail due to no longer supported np.object alias in current Numpy

Issue - State: closed - Opened by pcm32 over 1 year ago - 3 comments
Labels: bug

#476 - How to filter out motifs in reg.csv from pyscenic ctx

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

#475 - [BUG] 'Series' object has no attribute 'iteritems'

Issue - State: closed - Opened by crotoc over 1 year ago - 4 comments
Labels: bug

#474 - AttributeError: module 'numpy' has no attribute 'object'.[BUG]

Issue - State: closed - Opened by Li-ZhiD over 1 year ago
Labels: bug

#473 - Is this expected run time really expected?

Issue - State: open - Opened by li-xuyang28 over 1 year ago - 4 comments
Labels: question