Issues

• RECON2.2 gives far more flat-zero reaction penalties than RECON2_mat (75% vs. 33%) on identical human scRNA-seq data — expected, or a bug?

  YosefLab/Compass#124 · Filter by author VittoriaOssanna opened on Sep 18, 2026

• TypeError: an integer is required

  YosefLab/Compass#123 · Filter by author dnavi23 opened on Apr 10, 2025
  1

• Empty "reactions.tsv" output

  YosefLab/Compass#122 · Filter by author LeMon2582 opened on Feb 11, 2025
  1

• Does compass better separating the anndata by cell type?

  YosefLab/Compass#121 · Filter by author giuliaelgarcia opened on Dec 10, 2024

• COMPASS running so slowly!!!!

  YosefLab/Compass#120 · Filter by author wuxiangning opened on Nov 19, 2024
  3

• Can not install compass

  YosefLab/Compass#119 · Filter by author wuxiangning opened on Nov 19, 2024
  1

• What do the expected output files look like in COMPASS?

  YosefLab/Compass#116 · Filter by author skoturan opened on Oct 30, 2024

• Under pathological conditions, is it normal that all metabolic reactions are upregulated?

  YosefLab/Compass#114 · Filter by author jouska540 opened on Oct 9, 2024
  3

• multiprocessing.pool.MaybeEncodingError: Error sending result: '<multiprocessing.pool.ExceptionWithTraceback object at 0x7f840db71ee0>'. Reason: 'TypeError("cannot pickle 'SwigPyObject' object")'

  YosefLab/Compass#113 · Filter by author xwt778 opened on Sep 28, 2024
  1

• tested versions of dependencies for building compass docker image

  YosefLab/Compass#112 · Filter by author rajuadduri opened on Sep 11, 2024

• need for Docker image

  YosefLab/Compass#111 · Filter by author pengbo233 opened on Aug 13, 2024
  3

• normalization

  YosefLab/Compass#110 · Filter by author shimasadri opened on Jul 22, 2024
  1

• Seeking Guidance on Data Format (my own reaction and genes files from KEGG) Conversion for COMPASS Analysis

  YosefLab/Compass#108 · Filter by author ptdang1001 opened on Mar 26, 2024

• Are there any schematics to visualize where each reaction are at relative to each subsystem?

  YosefLab/Compass#107 · Filter by author ahdee opened on Mar 4, 2024
  1

• Metabolite secretion/uptake ?

  YosefLab/Compass#106 · Filter by author kmunozforti opened on Feb 24, 2024

• Analysis pipeline using RECON2.2 and metabolites

  YosefLab/Compass#105 · Filter by author kmunozforti opened on Feb 6, 2024

• AttributeError: 'DataFrame' object has no attribute 'iteritems'

  YosefLab/Compass#101 · Filter by author zhongguozhiwang opened on Nov 12, 2023
  7

• Can the software use GPU to calculate the reactions.txt. Because CPU is too slow.

  YosefLab/Compass#100 · Filter by author MedTiLab opened on Oct 28, 2023

• Application to UMI based technology

  YosefLab/Compass#99 · Filter by author Harry25R opened on Aug 15, 2023
  1

• Consider using GLPK instead of CPLEX

  YosefLab/Compass#98 · Filter by author ejames604 opened on Jun 29, 2023
  1

• installing cplex package

  YosefLab/Compass#97 · Filter by author ghost opened on Jun 19, 2023
  2

• Use Compass to solve a large amount of time-series bulk RNAseq data

  YosefLab/Compass#96 · Filter by author xiaowaileeli opened on Jun 15, 2023

• Run frozen at 0%

  YosefLab/Compass#95 · Filter by author brycemash opened on May 30, 2023
  2

• Compass analysis from Seurat subcluster - get_reaction_consistencies issue

  YosefLab/Compass#90 · Filter by author france-hub opened on Nov 29, 2022
  10

• Sample_name problem

  YosefLab/Compass#89 · Filter by author ZachLW opened on Nov 20, 2022
  2