Ecosyste.ms: Issues

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GitHub / aertslab/pySCENIC issues and pull requests

#601 - [BUG] problem with binarization not detecting bimodal correctly

Issue - State: open - Opened by Sirin24 27 days ago
Labels: bug

#600 - [BUG] Non-transcription factor gene “Fgf15” found in mm_mgi_tfs.txt

Issue - State: open - Opened by Ashone1992 about 1 month ago
Labels: bug

#599 - t-sne interpretation

Issue - State: open - Opened by robertzeibich about 1 month ago - 1 comment
Labels: question

#598 - t-sne on binary regulon activity

Issue - State: open - Opened by robertzeibich about 1 month ago
Labels: question

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

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

#596 - very long run time for very large dataset

Issue - State: open - Opened by baptisteavot-ukdri 3 months ago - 2 comments
Labels: bug

#595 - Results - After the "df2regulon" step of the tutorial

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

#594 - binarization

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

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

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

#591 - different targets different conditions

Issue - State: open - Opened by Sirin24 4 months ago

#590 - [BUG]pyscenic version conflict when using feather v2 vs v1

Issue - State: open - Opened by Chun-Hao025 4 months ago - 1 comment
Labels: bug

#589 - KeyError 'Field <GENE> does not exist in schema' at `prune2df` step for tutorial

Issue - State: open - Opened by tuanpham96 4 months ago - 4 comments
Labels: bug

#588 - output from singularity-pyscenic - downstream analysis

Issue - State: open - Opened by yulchen810 4 months ago
Labels: question

#587 - [results]about MotifSimilarityQvalue, OrthologousIdentity and Annotation in results

Issue - State: open - Opened by SYSUMSD 4 months ago - 1 comment
Labels: question

#586 - pyscenic ctx error - EOFError

Issue - State: open - Opened by yulchen810 4 months ago - 2 comments
Labels: bug

#585 - pyscenic grn: error: argument expression_mtx_fname

Issue - State: open - Opened by yulchen810 4 months ago - 1 comment
Labels: bug

#584 - [BUG]

Issue - State: open - Opened by aterceros 4 months ago - 2 comments
Labels: bug

#583 - unable to pull [ERROR]

Issue - State: open - Opened by yulchen810 4 months ago - 3 comments
Labels: bug

#581 - [BUG] The whole AUC matrix are 0 values

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

#580 - [issue] running pySCENIC on large datasets

Issue - State: open - Opened by li-xuyang28 5 months ago - 1 comment
Labels: question

#579 - [BUG]pyscenic error with numpy has no attribute 'object'

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

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

Issue - State: open - Opened by xyang2uchicago 5 months ago - 3 comments
Labels: bug

#576 - getAUC function error

Issue - State: closed - Opened by apal6 5 months ago - 1 comment
Labels: bug

#575 - binarize function error

Issue - State: open - Opened by apal6 5 months ago
Labels: bug

#574 - Database creation for Killifish

Issue - State: closed - Opened by juhi-ku 5 months ago - 1 comment

#573 - Correct TF File

Issue - State: open - Opened by amiramarouf 5 months ago - 1 comment
Labels: question

#572 - pyscenic aucell

Issue - State: closed - Opened by zznx 5 months ago - 3 comments
Labels: bug

#571 - Time pyscenic grn step in conda versus image

Issue - State: closed - Opened by Sirin24 6 months ago

#570 - compare between different conditions

Issue - State: open - Opened by Sirin24 6 months ago - 1 comment

#569 - Different batches/studies

Issue - State: open - Opened by Flu09 6 months ago - 2 comments

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

Issue - State: open - Opened by Flu09 6 months ago - 4 comments
Labels: question

#567 - [BUG] pyscenic grn and type error

Issue - State: open - Opened by tutu256 6 months ago - 1 comment
Labels: bug

#566 - IDs for TFs missing

Issue - State: open - Opened by chrarnold 6 months ago - 1 comment
Labels: bug

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

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

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

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

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

Issue - State: open - Opened by AAA-3 7 months ago - 9 comments
Labels: bug

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

Issue - State: open - Opened by jung233 7 months ago - 1 comment
Labels: bug

#559 - [BUG] run in pyscenic grn

Issue - State: open - Opened by zhangdong360 8 months ago - 11 comments
Labels: bug

#558 - ERROR - Error in Nanny killing Worker subprocess

Issue - State: closed - Opened by ASNbioinf 8 months ago - 1 comment
Labels: bug

#557 - [ERROR] in running Pyscenic GRN grnboost2

Issue - State: open - Opened by husain223 8 months ago - 3 comments
Labels: bug

#555 - ctx pyscenic Error

Issue - State: open - Opened by angelica-varesi 8 months ago - 1 comment
Labels: bug

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

Issue - State: open - Opened by lpalvin 8 months ago - 4 comments
Labels: bug

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

Issue - State: open - Opened by bitcometz 8 months ago - 6 comments
Labels: bug

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

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

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

Issue - State: open - Opened by Liripo 9 months ago - 1 comment
Labels: question

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

Issue - State: closed - Opened by Liripo 9 months ago
Labels: bug

#547 - CTX running infinitely long. Defunct child processes

Issue - State: closed - Opened by arunchakra 9 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 9 months ago - 2 comments
Labels: bug

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

Issue - State: open - Opened by yllahmu 10 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 10 months ago - 1 comment
Labels: question

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

Issue - State: open - Opened by juniajvs 10 months ago - 5 comments
Labels: bug

#542 - Regulon Specificity Scores Are Correlated With Size

Issue - State: closed - Opened by ggruenhagen3 10 months ago - 2 comments
Labels: bug

#541 - [question] hg19 tf list

Issue - State: open - Opened by colin893 10 months ago - 1 comment
Labels: bug

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

Issue - State: closed - Opened by HelloWorldLTY 10 months ago - 3 comments
Labels: bug

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

Issue - State: open - Opened by hansong798 11 months ago - 4 comments
Labels: question

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

Issue - State: open - Opened by QianLLLL 11 months ago
Labels: question

#536 - [BUG] Numpy Object Deprecation Error

Issue - State: closed - Opened by Tripfantasy 11 months ago - 5 comments
Labels: bug

#532 - /usr/bin/sh: 1: pyscenic: not found [BUG]

Issue - State: open - Opened by RolantusdataExp 11 months ago - 4 comments
Labels: bug

#530 - [BUG]exceeded distributed.worker_memory

Issue - State: open - Opened by xgqyoung 12 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 about 1 year ago - 6 comments
Labels: bug

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

Issue - State: open - Opened by Mira0507 about 1 year ago - 3 comments
Labels: bug

#525 - Error running GRNBoost2 step

Issue - State: open - Opened by eblchen about 1 year ago - 18 comments

#524 - large dataset failed

Issue - State: open - Opened by wangjiawen2013 about 1 year ago - 1 comment
Labels: bug

#523 - Scenic is not compatible with snakemake

Issue - State: open - Opened by wangjiawen2013 about 1 year ago - 6 comments
Labels: bug

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

Issue - State: open - Opened by asmlgkj about 1 year ago - 2 comments
Labels: bug

#521 - add_scenic_metadata error[BUG]

Issue - State: closed - Opened by AnjaliS1 about 1 year ago
Labels: bug

#520 - auc bug

Issue - State: open - Opened by AnjaliS1 about 1 year ago - 1 comment
Labels: bug

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

Issue - State: open - Opened by Jingle0814 about 1 year ago
Labels: question

#518 - [BUG] Installation error

Issue - State: open - Opened by as7a5 about 1 year ago - 3 comments
Labels: bug

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

Issue - State: open - Opened by stefanerb89 about 1 year ago
Labels: question

#516 - [results] Question about pySCENIC result

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

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

Issue - State: open - Opened by stefanerb89 about 1 year ago - 1 comment
Labels: bug

#511 - Similare Transcription factor in TF resources

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

#510 - pyscenic aucell command does not complete

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

#509 - df2regulons splitting gene names by character

Issue - State: closed - Opened by Tripfantasy over 1 year ago - 3 comments

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

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

#506 - [BUG]pyscenic ctx --no_pruning

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

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

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

#504 - [BUG] pyscenic grn

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

#503 - [BUG]error: 'OverflowError: cannot serialize a bytes object larger than 4 GiB'[ERROR]

Issue - State: open - Opened by liliyuan001 over 1 year ago - 2 comments
Labels: bug

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

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

#501 - How to use SCENIC analysis of yeast?

Issue - State: open - Opened by tuqiang2014 over 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