drisso/zinbwave

Issues

• Why are coefficients for feature covariates sample-dependent?

  #74 opened a year ago by clemenskreutz
  0

• zinbsurf taking forever

  #73 opened a year ago by eltonjrv
  1

• unable to find an inherited method for function ‘zinbFit’ for signature ‘"data.frame"’

  #72 opened 2 years ago by eltonjrv
  9

• Error in d$value$value : $ operator is invalid for atomic vectors

  #71 opened 2 years ago by IshaMonga
  0

• Sample 3 has only 0 counts!

  #70 opened 2 years ago by ambertrujillo
  0

• Meaning of the weights

  #69 opened 3 years ago by RonjaJohnen
  2

• Error in zinbwave

  #63 opened 3 years ago by ZHIDIHUAYUAN
  1

• What's the best way to adjust the sample batch covariable in the differential expression?

  #65 opened 3 years ago by Yunuuuu
  3

• Clarification on observation weights

  #68 opened 3 years ago by prajkta9
  1

• Negative values in normalizedValues output

  #67 opened 3 years ago by agranado
  2

• Index Error

  #51 opened 4 years ago by ChrisAi89
  2

• reducedDim() returns only 0

  #66 opened 4 years ago by yeroslaviz
  4

• model and K values in zinbwave + Deseq2

  #64 opened 4 years ago by AyanoNomura
  4

• zinbwave on integrated data set

  #62 opened 4 years ago by yeroslaviz
  1

• Computing observational weights in the zinbwave function using a sparse matrix

  #60 opened 4 years ago by rfarouni
  5

• How to work with duplicates?

  #61 opened 4 years ago by yeroslaviz
  2

• zinbwave Matrix error

  #45 opened 4 years ago by cstrlln
  6

• Error if add gene-level covariates

  #34 opened 6 years ago by rtian30
  3

• W2=0 when calculating two latent variables

  #59 opened 4 years ago by vincr04
  3

• Latent factors for differential expression

  #58 opened 4 years ago by vincr04
  1

• Zinbwave parallelization issue

  #38 opened 6 years ago by giovp
  10

• Change zinbwave's default value of K

  #57 opened 4 years ago by drisso
  1

• Scanpy AnnData Object as Input

  #50 opened 4 years ago by aditisk
  3

• Unsuccessful parameter recovery & unexpected distribution of estimated W values

  #23 opened 4 years ago by gbiele
  3

• Running zinbwave on cluster

  #27 opened 4 years ago by timydaley
  4

• zinbFit again stops with error

  #31 opened 4 years ago by friedue
  6

• zinbwave+Deseq2 Differential expression 10x

  #36 opened 4 years ago by bio-la
  3

• Error in getAndCheckWeights(object, modelMatrix) : all(weights.ok) is not TRUE

  #39 opened 4 years ago by bio-la
  1

• zinbwave design matrix

  #44 opened 4 years ago by JoannaTan
  3

• padjFilter column in edgeR results

  #55 opened 4 years ago by vincr04
  1

• Documentation error for "observationalWeights"

  #56 opened 4 years ago by rupertoverall
  1

• Decreasing log-likelihood with commondispersion = FALSE

  #54 opened 4 years ago by fedeago
  3

• Recovery of imputed values

  #53 opened 4 years ago by kmuench
  1

• Problem generating observational weights (zinbwave_1.8.0)

  #47 opened 5 years ago by bgrone
  5

• Strange BCV plot for 10x data

  #41 opened 5 years ago by lazappi
  13

• Normalized value negative correlation with bulk

  #46 opened 5 years ago by zji90
  4

• Bug in computeObservationWeights?

  #43 opened 5 years ago by drisso
  4

• ZinbWave + RSEC error

  #42 opened 5 years ago by siyao-liu
  1

• zinbAIC, zinbBIC functions seems to have got the rows and columns of the data matrix switched

  #40 opened 6 years ago by reubenthomas
  1

• So very slow, could you develop speed-ups using, e.g., Rcpp?

  #37 opened 6 years ago by chriscainx
  3

• Managing parallelism on cluster

  #35 opened 6 years ago by afinneg2
  3

• weights must be finite positive values

  #33 opened 6 years ago by ktroule
  13

• error when using large epsilon values

  #22 opened 6 years ago by gbiele
  7

• No weights after zinbwave()

  #32 opened 6 years ago by ktroule
  2

• Verbose mode prints wrong value of log likelihood

  #30 opened 6 years ago by drisso
  1

• normalization with 5000 or 10000 filtered genes

  #29 opened 6 years ago by abasseville
  4

• Can't run zinbwave in R

  #28 opened 6 years ago by yingzhang121
  3

• Gene loadings

  #26 opened 6 years ago by bio-la
  2

• maximal number of DLLs reached

  #25 opened 6 years ago by bio-la
  3

• zinbFit parallel windows 7

  #24 opened 6 years ago by XiangZhangSC
  4