drisso zinbwave issues - Githubissues

drisso / zinbwave

Clone of the Bioconductor repository for the zinbwave package, see https://bioconductor.org/packages/zinbwave

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Why are coefficients for feature covariates sample-dependent?

#74 clemenskreutz opened 1 year ago
0
zinbsurf taking forever

#73 eltonjrv closed 1 year ago
1
unable to find an inherited method for function ‘zinbFit’ for signature ‘"data.frame"’

#72 eltonjrv closed 1 year ago
9
Error in d$value$value : $ operator is invalid for atomic vectors

#71 IshaMonga opened 1 year ago
0
Sample 3 has only 0 counts!

#70 ambertrujillo opened 2 years ago
1
Meaning of the weights

#69 RonjaJohnen closed 3 years ago
2
Clarification on observation weights

#68 prajkta9 closed 3 years ago
1
Negative values in normalizedValues output

#67 agranado closed 3 years ago
2
reducedDim() returns only 0

#66 yeroslaviz closed 4 years ago
4
What's the best way to adjust the sample batch covariable in the differential expression?

#65 Yunuuuu closed 3 years ago
3
model and K values in zinbwave + Deseq2

#64 AyanoNomura opened 4 years ago
5
Error in zinbwave

#63 ZHIDIHUAYUAN closed 3 years ago
1
zinbwave on integrated data set

#62 yeroslaviz closed 4 years ago
1
How to work with duplicates?

#61 yeroslaviz closed 4 years ago
2
Computing observational weights in the zinbwave function using a sparse matrix

#60 rfarouni opened 4 years ago
5
W2=0 when calculating two latent variables

#59 vincr04 closed 4 years ago
3
Latent factors for differential expression

#58 vincr04 closed 4 years ago
1
Change zinbwave's default value of K

#57 drisso closed 4 years ago
1
Documentation error for "observationalWeights"

#56 rupertoverall closed 4 years ago
1
padjFilter column in edgeR results

#55 vincr04 closed 4 years ago
1
Decreasing log-likelihood with commondispersion = FALSE

#54 fedeago closed 4 years ago
3
Recovery of imputed values

#53 kmuench closed 4 years ago
1
Adding beta parameter when it uses SolveRidgeRegression function

#52 fedeago closed 4 years ago
3
Index Error

#51 ChrisAi89 closed 4 years ago
2
Scanpy AnnData Object as Input

#50 aditisk closed 4 years ago
3
added 0 element in nleft; this way correct columns are removed from n…

#49 SzMK closed 4 years ago
4
zinbsurf no longer fails for formula ~1 due to lack of drop=FALSE arg…

#48 SzMK closed 4 years ago
1
Problem generating observational weights (zinbwave_1.8.0)

#47 bgrone closed 5 years ago
5
Normalized value negative correlation with bulk

#46 zji90 closed 5 years ago
4
zinbwave Matrix error

#45 cstrlln closed 4 years ago
6
zinbwave design matrix

#44 JoannaTan closed 4 years ago
3
Bug in computeObservationWeights?

#43 drisso closed 5 years ago
4
ZinbWave + RSEC error

#42 siyao-liu closed 5 years ago
1
Strange BCV plot for 10x data

#41 lazappi opened 5 years ago
13
zinbAIC, zinbBIC functions seems to have got the rows and columns of the data matrix switched

#40 reubenthomas opened 5 years ago
1
Error in getAndCheckWeights(object, modelMatrix) : all(weights.ok) is not TRUE

#39 bio-la closed 4 years ago
1
Zinbwave parallelization issue

#38 giovp opened 6 years ago
11
So very slow, could you develop speed-ups using, e.g., Rcpp?

#37 chriscainx closed 6 years ago
3
zinbwave+Deseq2 Differential expression 10x

#36 bio-la closed 4 years ago
3
Managing parallelism on cluster

#35 afinneg2 closed 6 years ago
3
Error if add gene-level covariates

#34 rtian30 opened 6 years ago
3
weights must be finite positive values

#33 ktroule closed 6 years ago
13
No weights after zinbwave()

#32 ktroule closed 6 years ago
2
zinbFit again stops with error

#31 friedue closed 4 years ago
6
Verbose mode prints wrong value of log likelihood

#30 drisso closed 6 years ago
1
normalization with 5000 or 10000 filtered genes

#29 abasseville closed 6 years ago
4
Can't run zinbwave in R

#28 yingzhang121 closed 6 years ago
3
Running zinbwave on cluster

#27 timydaley closed 4 years ago
4
Gene loadings

#26 bio-la closed 6 years ago
2
maximal number of DLLs reached

#25 bio-la closed 6 years ago
3