YosefLab/Compass

Issues

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

  #113 opened a month ago by xwt778
  0

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

  #92 opened 2 years ago by JoelHaas
  7

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

  #101 opened a year ago by zhongguozhiwang
  7

• tested versions of dependencies for building compass docker image

  #112 opened 2 months ago by rajuadduri
  0

• need for Docker image

  #111 opened 3 months ago by pengbo233
  1

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

  #107 opened 8 months ago by ahdee
  1

• No module named 'compass_analysis'

  #83 opened 3 months ago by muralyv
  2

• Can the interrupted Compass code continue to run?

  #85 opened 3 months ago by qiuju-Zhang
  2

• normalization

  #110 opened 3 months ago by shimasadri
  1

• Consider using GLPK instead of CPLEX

  #98 opened a year ago by emyr666
  1

• Reason: 'TypeError("cannot pickle 'SwigPyObject' object")'

  #91 opened 4 months ago by hello257
  4

• Numeric entry is not a double precision number (NaN)

  #84 opened 2 years ago by littleju777
  1

• 'TypeError("cannot pickle 'SwigPyObject' object")'

  #109 opened 6 months ago by Ronvaknins
  1

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

  #108 opened 7 months ago by ptdang1001
  0

• Reactions output file identical values

  #104 opened 8 months ago by kmunozforti
  0

• Metabolite secretion/uptake ?

  #106 opened 8 months ago by kmunozforti
  0

• Analysis pipeline using RECON2.2 and metabolites

  #105 opened 9 months ago by kmunozforti
  0

• Pseudo-bulk or mixed-effects modeling approach to differential testing of reaction scores

  #103 opened 10 months ago by mariecrane
  1

• Run frozen at 0%

  #95 opened a year ago by brycemash
  1

• CPLEX academic version "Page Not Found"

  #102 opened a year ago by mebbert
  3

• Compass analysis from Seurat subcluster - get_reaction_consistencies issue

  #90 opened 2 years ago by france-hub
  9

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

  #100 opened a year ago by YzGLab
  0

• Application to UMI based technology

  #99 opened a year ago by Harry25R
  0

• Is Recon3D version 3.01 suitable for model construction?

  #76 opened 2 years ago by MingwuDuan
  1

• installing cplex package

  #97 opened a year ago by bakhtiararya
  0

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

  #96 opened a year ago by xiaowaileeli
  0

• How to correctly get data from seurat object

  #94 opened a year ago by brycemash
  0

• Fixed

  #93 opened a year ago by brycemash
  0

• Sample_name problem

  #89 opened 2 years ago by ZachLW
  2

• where can I get more information about labeled_reactions?

  #87 opened 2 years ago by qiuju-Zhang
  1

• Simulating pharmacologic inhibition through FBA?

  #88 opened 2 years ago by agirgis3
  0

• TypeError: alpha must be a float or None when Figure 2E replication

  #75 opened 2 years ago by Roger-GOAT
  2

• multiprocessing.pool error or CPLEX error (DEMO file)

  #86 opened 2 years ago by jiangzh-coder
  1

• How to interpreter the Compass results?

  #77 opened 2 years ago by Zessi-C
  1

• running Compass from a Singularity image

  #67 opened 2 years ago by hmassalha
  3

• CPLEX - data size issue

  #80 opened 2 years ago by sid5427
  1

• how to run model recon3 in recon3-misc branch?

  #82 opened 2 years ago by Roger-GOAT
  0

• How to do differential reaction activity analysis between samples in two conditions?

  #81 opened 2 years ago by wang-tan
  0

• How to interpret reactions in GSMM without genes associated in annotation?

  #79 opened 2 years ago by kpruss
  0

• expression.tsv has reactions in place of gene symbol. Gene symbol is also misspelled.

  #78 opened 2 years ago by j2r2jones
  0

• how to deal with batch effect

  #71 opened 2 years ago by Fengzs1997
  1

• Compass on data with batch effect

  #63 opened 3 years ago by Chengwei94
  1

• seperate runs

  #74 opened 2 years ago by gneedle1
  0

• wilcox_results show error: KeyError: "Passing list-likes to .loc or [] with any missing labels is no longer supported.

  #73 opened 2 years ago by Roger-GOAT
  0

• Completely identical reaction penalties for samples - is that possible?

  #72 opened 2 years ago by loganminhdang
  0

• TypeError("cannot pickle 'SwigPyObject' object")

  #64 opened 3 years ago by garricklu
  1

• Tutorial is not match your code now,,,,,,

  #70 opened 2 years ago by bxxfl
  0

• Using Compass with Bulk RNA-seq

  #69 opened 2 years ago by gepmat
  1

• Post-processing of secretion / uptake values

  #68 opened 2 years ago by linus235
  0

• Problem while building up model cache

  #65 opened 3 years ago by michallipinski
  0