theislab/scCODA

Issues

• What is the reasonable FDR value? 0.05?

  #102 opened 2 months ago by mainharryHR
  1

• Multiple comparisons

  #97 opened 2 months ago by mainharryHR
  2

• Using continuous variables yield weird results.

  #96 opened 2 months ago by Marwansha
  3

• Value Error when runing mod.CompositionalAnalysis

  #101 opened 2 months ago by boluofen
  7

• alr t test

  #100 opened 2 months ago by feanaros
  3

• Intra-sample abundances

  #99 opened 3 months ago by n-hal
  1

• How to plot the final result?

  #98 opened 4 months ago by mainharryHR
  1

• mixed effect model

  #87 opened 4 months ago by t-a-m-i
  1

• Use the model with multiple covariants including numeric ones?

  #88 opened 4 months ago by RunyuXia
  1

• interpreting the output with the issue of compositionality.

  #93 opened 4 months ago by Marwansha
  6

• How to compare multiple groups with sccoda

  #94 opened 4 months ago by karenlawwc
  7

• Bug in viz.boxplots function (and possibly others)

  #95 opened 7 months ago by reemagit
  3

• module 'pertpy.plot' has no attribute 'coda'

  #92 opened 7 months ago by Marwansha
  1

• Influence of number of cells in parameterization

  #91 opened 7 months ago by auesro
  6

• Usage without replicates ?

  #90 opened 8 months ago by divyanshusrivastava
  2

• Covariate has non-unique values

  #89 opened 8 months ago by schroeme
  2

• Different results for same comparison, based on which group is selected as reference

  #86 opened 8 months ago by mareymessi
  2

• Tutorial for R/reticulate

  #83 opened 8 months ago by ConDem94
  3

• model comparison using LOO/WAIC

  #82 opened 8 months ago by hoeflerb
  2

• Exporting Summary Results

  #80 opened 8 months ago by antonio-miranda
  1

• Questions about generalizability to other NGS datasets

  #77 opened 8 months ago by jolespin
  1

• scCODA p-values?

  #72 opened 8 months ago by katieaney
  1

• Feature Request: log10 scaling for Boxplots

  #69 opened 8 months ago by alefrol638
  1

• loading data with dat.from_scanpy

  #65 opened 2 years ago by HosseinMousavi
  2

• Additive model with batch

  #85 opened a year ago by flde
  2

• Final Parameter and log2-fold change have different signs

  #84 opened a year ago by PauBadiaM
  6

• additive effects and interaction terms

  #81 opened a year ago by hoeflerb
  3

• Error when num_burnins > num_results

  #79 opened a year ago by dawe
  4

• conda compatibility

  #75 opened a year ago by Nusob888
  4

• Which tensorflow version to use?

  #58 opened 2 years ago by c-westhoven
  3

• AttributeError: module 'arviz' has no attribute 'data'

  #78 opened a year ago by jhong26
  2

• TypeError: '<' not supported between instances of 'str' and 'int' on toy dataset

  #76 opened 2 years ago by jolespin
  1

• Bootstrap or splitting my samples

  #74 opened 2 years ago by dekan-aleksandr
  2

• Replace sklearn dependency with scikit-learn

  #73 opened 2 years ago by radutanasa
  1

• access sim_results.summary() for further analysis in R

  #71 opened 2 years ago by dwendisch
  2

• Importance of warnings/errors in model_scelltype_Time.sample_hmc() output

  #54 opened 2 years ago by Lopiniatre
  1

• Feature Request: Automatically print significance indicator in boxplots

  #70 opened 2 years ago by alefrol638
  1

• All cell types as reference loop error

  #68 opened 2 years ago by AClab-sgarcia
  17

• Understanding inclusion probability

  #67 opened 2 years ago by auesro
  4

• Zero log2-fold change but credible change being identified?

  #66 opened 2 years ago by learning-MD
  3

• Cell identities displaying as numbers?

  #64 opened 2 years ago by potterae
  1

• WARNING:tensorflow:@custom_gradient grad_fn has 'variables' in signature, but no ResourceVariables were used on the forward pass.

  #63 opened 2 years ago by bobosfw
  1

• est_fdr did not change the result

  #62 opened 2 years ago by grimwoo
  6

• P value (FDR) and interpretation of "Final Parameter"

  #61 opened 2 years ago by grimwoo
  2

• Is the input data expected by scCODA the size of the cell type for each sample?

  #60 opened 2 years ago by altairwei
  1

• col_wrap in utils.visualization.boxplots

  #55 opened 2 years ago by c-westhoven
  1

• Influence of subtypes present in the dataset

  #57 opened 2 years ago by auesro
  4

• WARNING:tensorflow:@custom_gradient grad_fn has 'variables' in signature, but no ResourceVariables were used on the forward pass.

  #56 opened 2 years ago by auesro
  2

• Looping over cell types to use as reference: discrepancy?

  #53 opened 2 years ago by koenvandenberge
  11

• verbose option for `sample_hmc`

  #52 opened 2 years ago by koenvandenberge
  1